Chemical compounds, compositions and methods for kinase modulation

ABSTRACT

Chemical compounds that modulate kinase activity, including PI3 kinase activity, and chemical compounds, pharmaceutical compositions, and methods of treatment of diseases and conditions associated with kinase activity, including P13 kinase activity, are described herein.

CLAIM OF PRIORITY

This application claims priority from U.S. Ser. No. 61/347,370, filedMay 21, 2010, which is incorporated herein by reference in its entirety.

BACKGROUND

The activity of cells can be regulated by external signals thatstimulate or inhibit intracellular events. The process by whichstimulatory or inhibitory signals are transmitted into and within a cellto elicit an intracellular response is referred to as signaltransduction. Over the past decades, cascades of signal transductionevents have been elucidated and found to play a central role in avariety of biological responses. Defects in various components of signaltransduction pathways have been found to account for a vast number ofdiseases, including numerous forms of cancer, inflammatory disorders,metabolic disorders, vascular and neuronal diseases (Gaestel et al.Current Medicinal Chemistry (2007) 14:2214-2234).

Kinases represent a class of important signaling molecules. Kinases cangenerally be classified into protein kinases and lipid kinases, andcertain kinases exhibit dual specificities. Protein kinases are enzymesthat phosphorylate other proteins and/or themselves (i.e.,autophosphorylation). Protein kinases can be generally classified intothree major groups based upon their substrate utilization: tyrosinekinases which predominantly phosphorylate substrates on tyrosineresidues (e.g., erb2, PDGF receptor, EGF receptor, VEGF receptor, src,abl), serine/threonine kinases which predominantly phosphorylatesubstrates on serine and/or threonine residues (e.g., mTorC1, mTorC2,ATM, ATR, DNA-PK, Akt), and dual-specificity kinases which phosphorylatesubstrates on tyrosine, serine and/or threonine residues.

Lipid kinases are enzymes that catalyze the phosphorylation of lipids.These enzymes, and the resulting phosphorylated lipids and lipid-derivedbiologically active organic molecules, play a role in many differentphysiological processes, including cell proliferation, migration,adhesion, and differentiation. Certain lipid kinases are membraneassociated and they catalyze the phosphorylation of lipids contained inor associated with cell membranes. Examples of such enzymes includephosphoinositide(s) kinases (e.g., PI3-kinases, PI4-Kinases),diacylglycerol kinases, and sphingosine kinases.

The phosphoinositide 3-kinases (PI3Ks) signaling pathway is one of themost highly mutated systems in human cancers. PI3K signaling is also akey factor in many other diseases in humans. PI3K signaling is involvedin many disease states including allergic contact dermatitis, rheumatoidarthritis, osteoarthritis, inflammatory bowel diseases, chronicobstructive pulmonary disorder, psoriasis, multiple sclerosis, asthma,disorders related to diabetic complications, and inflammatorycomplications of the cardiovascular system such as acute coronarysyndrome.

PI3Ks are members of a unique and conserved family of intracellularlipid kinases that phosphorylate the 3′-OH group onphosphatidylinositols or phosphoinositides. The PI3K family comprises 15kinases with distinct substrate specificities, expression patterns, andmodes of regulation. The class I PI3Ks (p110α, p110β, p110δ, and p110γ)are typically activated by tyrosine kinases or G-protein coupledreceptors to generate PIP3, which engages downstream effectors such asthose in the Akt/PDK1 pathway, mTOR, the Tec family kinases, and the Rhofamily GTPases. The class II and III PI3Ks play a key role inintracellular trafficking through the synthesis of PI(3)P and PI(3,4)P2.The PI3Ks are protein kinases that control cell growth (mTORC1) ormonitor genomic integrity (ATM, ATR, DNA-PK, and hSmg-1).

The delta (δ) isoform of class I PI3K has been implicated, inparticular, in a number of diseases and biological processes. PI3K δ isexpressed primarily in hematopoietic cells including leukocytes such asT-cells, dendritic cells, neutrophils, mast cells, B-cells, andmacrophages. PI3K δ is integrally involved in mammalian immune systemfunctions such as T-cell function, B-cell activation, mast cellactivation, dendritic cell function, and neutrophil activity. Due to itsintegral role in immune system function, PI3K δ is also involved in anumber of diseases related to undesirable immune response such asallergic reactions, inflammatory diseases, inflammation mediatedangiogenesis, rheumatoid arthritis, and auto-immune diseases such aslupus, asthma, emphysema and other respiratory diseases. Other class IPI3K involved in immune system function includes PI3K γ, which plays arole in leukocyte signaling and has been implicated in inflammation,rheumatoid arthritis, and autoimmune diseases such as lupus.

Unlike PI3K δ, the beta (β) isoform of class I PI3K appears to beubiquitously expressed. PI3K β has been implicated primarily in varioustypes of cancer including PTEN-negative cancer (Edgar et al. CancerResearch (2010) 70(3):1164-1172), and HER2-overexpressing cancer such asbreast cancer and ovarian cancer.

SUMMARY

As such, there remains a need for PI3K inhibitors capable of selectivelyinhibiting certain isoform(s) of class I PI3K without substantiallyaffecting the activity of the remaining isoforms of the same class. Inparticular, inhibitors capable of selectively inhibiting PI3K δ and/orPI3K γ, but without substantially affecting the activity of PI3K β,would reduce one or more possible side effects associated withunnecessary down-regulation of PI3K β activity in a subject. Suchinhibitors would be effective in ameliorating disease conditionsmediated primarily by PI3K δ/γ. The present disclosure addresses thisneed and provides related advantages as well.

In one aspect, provided herein is a compound of Formula I:

or pharmaceutically acceptable forms thereof, wherein,W_(a) ² is CR⁵ or N; W_(a) ³ is CR⁶ or N; W_(a) ⁴ is CR⁷ or N; whereinno more than two adjacent ring atoms selected from W_(a) ², W_(a) ³, andW_(a) ⁴ are heteroatoms;B is hydrogen, alkyl, amino, heteroalkyl, or a moiety of formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, andq is an integer of 0, 1, 2, 3, or 4;X is absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4;Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—,—N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is aninteger of 1, 2, 3, or 4;R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl,sulfonamido, halo, cyano, or nitro;each R² is independently alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate;R³ is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl,aralkyl, heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ isa heteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl, or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³;R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano, alkyl oramino;each R⁹ is independently hydrogen, alkyl, or heterocycloalkyl;

W_(d) is

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate;R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl, halo, —C(O)NH₂,aryl, heteroaryl, nonaromatic heterocyclyl, or cycloalkyl,R^(a′) is hydrogen, alkyl, —NH₂, cyano, or halogen; andeach R¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy, orhalogen.

In certain embodiments, compounds are provided of the following FormulaIb:

or pharmaceutically acceptable forms thereof, whereinB is hydrogen, alkyl, amino, heteroalkyl, or a moiety of Formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl;q is an integer of 0, 1, 2, 3, or 4;X is absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4;Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—,—N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is aninteger of 1, 2, 3, or 4;R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl,sulfonamido, halo, cyano, or nitro;each R² is independently alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate;R³ is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl,aralkyl, heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ isa heteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl, or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³;R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano, alkyl oramino;each R⁹ is independently hydrogen, alkyl, or heterocycloalkyl;

W_(d) is

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate;R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl, halo, —C(O)NH₂,aryl, heteroaryl, nonaromatic heterocyclyl, or cycloalkyl,R^(a′) is hydrogen, alkyl, —NH₂, cyano or halogen; andeach R¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy orhalogen.

In certain embodiments, R³ is selected from a 5-membered heteroaryl;5-membered nonaromatic heterocycle; 6-membered aryl; 6-memberedheteroaryl; 6-membered nonaromatic heterocycle; fused 5/6-bicyclicheteroaryl; fused 5/6-bicyclic nonaromatic heterocycle; C₁-C₆ alkylgroup substituted with a 5-membered heteroaryl, a 5-membered nonaromaticheterocycle, a 6-membered aryl or heteroaryl, a 6-membered nonaromaticheterocycle, a fused 5/6-bicyclic heteroaryl, or a fused 5/6-bicyclicnonaromatic heterocycle. In some embodiments, R³ is a heteroatomselected from N, S, and O, wherein the heteroatom has a covalent bondeither directly or through a C₁-C₆ alkyl group to a 5-memberedheteroaryl, a 5-membered nonaromatic heterocycle, a 6-membered aryl orheteroaryl, a 6-membered nonaromatic heterocycle, a fused 5/6-bicyclicheteroaryl, or a fused 5/6-bicyclic nonaromatic heterocycle. In someembodiments, R³ is a C₁-C₆ alkyl group substituted with a fusedpolycyclic group, wherein the polycyclic group has greater than tworings and is carbocyclic or heterocyclic; C₁-C₆ alkyl group substitutedwith a bridged cycloalkyl or bridged heterocyclic group. In someembodiments, R³ is C₁-C₆ alkyl group substituted with a spirocycliccycloalkyl or spirocyclic heterocyclic group. In some embodiments, R³ isa branched C₄-C₁₂ alkyl group, wherein said branched alkyl groupcontains at least one terminal t-butyl group.

In some embodiments, R³ is a 5-membered heteroaryl. In some embodiments,R³ is a 5-membered nonaromatic heterocycle. In some embodiments, R³ is a6-membered aryl. In some embodiments, R³ is a 6-membered heteroaryl. Insome embodiments, R³ is a 6-membered nonaromatic heterocycle. In someembodiments, R³ is a fused 5/6-bicyclic heteroaryl. In some embodiments,R³ is a fused 5/6-bicyclic nonaromatic heterocycle. In some embodiments,R³ is a 5-membered heteroaralkyl. In some embodiments, R³ is a5-membered nonaromatic heterocyclylalkyl. In some embodiments, R³ is a6-membered araralkyl. In some embodiments, R³ is a 6-memberedheteroaralkyl. In some embodiments, R³ is a 6-membered nonaromaticheterocyclylalkyl. In some embodiments, R³ is a fused 5/6-bicyclicheteroaralkyl. In some embodiments, R³ is a fused 5/6-bicyclicnonaromatic heterocyclylalkyl.

In certain embodiments, R³ is a heteroatom selected from N, S, and O,wherein the heteroatom has a covalent bond either directly or through aC₁-C₆ alkyl group to an aryl, heteroaryl or heterocyclyl. In someembodiments, R³ is N, wherein the N has a covalent bond either directlyor through a C₁-C₆ alkyl group to an aryl, heteroaryl or heterocyclyl.In some embodiments, R³ is N, wherein the N has a covalent bond directlyto an aryl, heteroaryl or heterocyclyl. In some embodiments, R³ is N,wherein N has a covalent bond directly to a heterocyclyl. In someembodiments, the heterocyclyl is 4-tetrahydro-2H-pyran. In someembodiments, R³ is

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is C₁₋₆ alkyl (e.g., methyl).

In certain embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is C₁₋₆ alkyl(e.g., methyl).

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is C₁₋₆ alkyl(e.g., methyl).

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is C₁₋₆ alkyl(e.g., methyl).

In certain embodiments, R³ is

In some embodiments, R¹³ is H.

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is C₁₋₆ alkyl (e.g., methyl). In someembodiments R¹³ is H.

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is C₁₋₆ alkyl(e.g., methyl).

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is halogen(e.g., fluoro).

In certain embodiments, R³ is

In some embodiments, R³ is

In some embodiments, R¹³ is H. In some embodiments, R¹³ is alkoxy (e.g.,methoxy).

In certain embodiments, R³ and R⁵ taken together with the carbons towhich they are attached can form a 5- or 6-membered ring which can besubstituted with 0, 1, 2, or 3 R¹³ groups.

In certain embodiments, B is hydrogen. In certain embodiments, acompound is provided of the previous formula wherein B is a moiety ofFormula II:

In some embodiments, W_(c) is aryl or heteroaryl. In some embodiments,W_(c) is 6-membered aryl (e.g., phenyl). In some embodiments, q is 0. Insome embodiments, R¹ is hydrogen. In some embodiments, q is 1. In someembodiments, R² is halo (e.g., fluoro).

In some embodiments, W_(c) is cycloalkyl (e.g., cyclopropyl). In someembodiments, q is 0. In some embodiments, R₁ is hydrogen.

In certain embodiments, Y is absent. In some embodiments, X is—(CH(R⁹))_(z)—. In some embodiments, z is 1. In some embodiments, R⁹ isindependently hydrogen. In some embodiments, R⁹ is independently alkyl(e.g., methyl).

In certain embodiments, W_(d) is

In some embodiments, R^(a′) is hydrogen. In some embodiments, R^(a′) is—NH₂.

In some embodiments, W_(d) is

In some embodiments, R¹² is halogen (e.g., fluoro). In some embodiments,R¹² is cyano. In some embodiments, R¹² is —C(O)NH₂. In some embodiments,R^(a′) is hydrogen.

In some embodiments, W_(d) is

In some embodiments, R^(a′) is —NH₂. In some embodiments, R¹² is halo(e.g., fluoro or iodo). In some embodiments, R¹² is cyano. In someembodiments, R¹² is haloalkyl (e.g., trifluoromethyl).

In certain embodiments, W_(d) is

In some embodiments, R^(a′) is cyano. In some embodiments, R¹² is —NH₂.

In some embodiments, W_(d) is

In some embodiments, W_(d) is

In certain embodiments, R³ is

In some embodiments, R^(a′) is —NH₂. In some embodiments, R¹² ishydrogen.

In certain embodiments, R⁶ is hydrogen. In some embodiments, R⁷ ishydrogen. In some embodiments, R⁸ is hydrogen. In some embodiments, R⁶,R⁷ and R⁸ are hydrogen.

In certain aspects, a compound is provided of formulae I or Ib wherein Bis a moiety of Formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl; q isan integer of 0 or 1; R¹ is hydrogen, alkyl, or halo; R² is alkyl orhalo; and R³ is a 5-membered heteroaryl, 6-membered heteroaryl, or fused5/6-bicyclic heteroaryl group.

In certain aspects, a compound is provided of formulae I or Ib wherein Bis a moiety of formula:

wherein W_(c) is aryl or cycloalkyl. In various embodiments, R³ containsone or two nitrogen atoms, with the proviso that non-nitrogenheteroatoms can be excluded. In various embodiments, R³ is a substitutedor unsubstituted group selected from phenyl, pyridine, pyrazole,piperazine, imidazole and pyrrolidine. For example, the R³ group can besubstituted with a C₁-C₆ alkyl group or a halogen.

In some embodiments of the compound of Formula I, Y is absent and W_(d)is:

In other embodiments, Y is present and W_(d) is:

In some embodiments, a compound is provided wherein the compound has astructure of Formula IV-A:

In certain embodiments, R¹² is monocyclic heteroaryl, bicyclicheteroaryl, or nonaromatic heterocyclyl. For example, R¹² can be asubstituted benzoxazole. In certain embodiments, R³ is a substituted orunsubstituted group selected from pyridine, pyrazole, piperazine, andpyrrolidine. The R³ group can be substituted with a C₁-C₆ alkyl group ora halogen.

In some embodiments, a compound of any of the above formulae is providedwherein X is —(CH(R⁹))_(z)—, wherein R⁹ is methyl and z=1; and W_(d) is

Accordingly, in some embodiments, the compound has one stereocenter,wherein said stereocenter can be in an (S)-stereochemical configurationor an (R)-stereochemical configuration. In some embodiments, a compoundis provided wherein the compound has a structure of Formula V-A2:

In certain embodiments, a compound described herein (e.g., a compound ofFormula V-A2) is present in a racemic mixture (e.g., less than about 10%enantiomeric excess of either the R or S stereoisomer). In someembodiments, a compound described herein (e.g., a compound of FormulaV-A2) is present in an enantiomeric excess of the R stereoisomer (e.g.,about 10%, 50%, 75%, 85%, 90%, 95%, 97%, 99% or greater). In someembodiments, a compound described herein (e.g., a compound of FormulaV-A2) is present in an enantiomeric excess of the S stereoisomer (e.g.,about 10%, 50%, 75%, 85%, 90%, 95%, 97%, 99% or greater).

In certain embodiments, R³ is phenyl, pyridine, pyrazole, piperazine,imidazole or pyrrolidine, substituted with 0, 1, 2, or 3 occurrences ofR¹³. In some embodiments, R¹³ is C₁-C₆ alkyl (e.g., methyl). In someembodiments, R¹³ is halogen (e.g., fluoro).

In some embodiments, a compound is provided wherein R³ is selected froma 5-membered heteroaryl selected from pyrrole, a furan, a thiazole, atriazole, a tetrazole and a thiophene group; a 5-membered nonaromaticheterocycle selected from pyrrolidine, a tetrahydrofuran, and atetrahydrothiophene group; a 6-membered heteroaryl selected frompyridine, pyrazine, pyrimidine, and pyridazine; a 6-membered nonaromaticheterocycle selected from piperidine, tetrahydropyran, and thiane; and afused 5/6-bicyclic heteroaryl selected from indole, isoindole,benzofuran, isobenzofuran, benzothiophene, benzothiazole, benzimidazole,indazole, benzoxazole, benzisoxazole, and purine; each of which can besubstituted with 0, 1, 2, or 3 occurrences of R¹³. In certainembodiments, R³ is selected from pyridine, pyrazole, piperazine, andpyrrolidine; each of which can be substituted with 0, 1, 2, or 3occurrences of R¹³. In some embodiments, R³ can be substituted with R¹³,which is C₁-C₆ alkyl (e.g., methyl) or a halogen (e.g., fluoro). In someembodiments, a compound is provided wherein R³ is selected from

wherein R¹³ is H C₁-C₆ alkyl (e.g., methyl) or halo (e.g., fluoro). Insome embodiments, R¹³ is C₁-C₆ alkyl (e.g., methyl). In someembodiments, R¹³ is halo (e.g., fluoro).

In some embodiments, R³ is selected from:

In certain embodiments, B is a moiety of Formula II:

wherein W_(c) is aryl or cycloalkyl. In certain embodiments, W_(d) isselected from

wherein R³ can be selected from pyridine, pyrazole, piperazine, andpyrrolidine; each of which can be substituted with 0, 1, 2, or 3occurrences of R¹³;B can be a moiety of Formula II:

wherein W_(c) is aryl or cycloalkyl; andW_(d) is selected from

In certain embodiments, R¹³ is C₁-C₆ alkyl (e.g., methyl) or a halogen(e.g., fluoro).

In certain embodiments, a compound as disclosed herein selectivelymodulates phosphatidyl inositol-3 kinase (PI3 kinase) delta isoform. Incertain embodiments, the compound selectively inhibits the delta isoformover the beta isoform. By way of non-limiting example, the ratio ofselectivity can be greater than a factor of about 10, greater than afactor of about 50, greater than a factor of about 100, greater than afactor of about 200, greater than a factor of about 400, greater than afactor of about 600, greater than a factor of about 800, greater than afactor of about 1000, greater than a factor of about 1500, greater thana factor of about 2000, greater than a factor of about 5000, greaterthan a factor of about 10,000, or greater than a factor of about 20,000,where selectivity can be measured by IC₅₀, among other means. In certainembodiments, the PI3 kinase delta isoform IC₅₀ activity of a compound asdisclosed herein can be less than about 1000 nM, less than about 100 nM,less than about 10 nM, or less than about 1 nM.

In certain embodiments, provided herein is a composition (e.g., apharmaceutical composition) comprising a compound as described hereinand a pharmaceutically acceptable excipient. In some embodiments,provided herein is a method of inhibiting a phosphatidyl inositol-3kinase (PI3 kinase), comprising contacting the PI3 kinase with aneffective amount of a compound or pharmaceutical composition asdescribed herein. In certain embodiments, a method is provided forinhibiting a phosphatidyl inositol-3 kinase (PI3 kinase) wherein saidPI3 kinase is present in a cell. The inhibition can take place in asubject suffering from a disorder selected from cancer, bone disorder,inflammatory disease, immune disease, nervous system disease, metabolicdisease, respiratory disease, thrombosis, and cardiac disease. Incertain embodiments, a second therapeutic agent is administered to thesubject.

In certain embodiments, a method is provided of selectively inhibiting aphosphatidyl inositol-3 kinase (PI3 kinase) delta isoform over PI3kinase beta isoform wherein the inhibition takes place in a cell.Non-limiting examples of the methods disclosed herein can comprisecontacting PI3 kinase delta isoform with an effective amount of acompound or pharmaceutical composition as disclosed herein. In anembodiment, such contact can occur in a cell.

In certain embodiments, a method is provided of selectively inhibiting aphosphatidyl inositol-3 kinase (PI3 kinase) delta isoform over PI3kinase beta isoform wherein the inhibition takes place in a subjectsuffering from a disorder selected from cancer, bone disorder,inflammatory disease, immune disease, nervous system disease, metabolicdisease, respiratory disease, thrombosis, and cardiac disease, saidmethod comprising administering an effective amount of a compound orpharmaceutical composition to said subject. In certain embodiments,provided herein is a method of treating a subject suffering from adisorder associated with phosphatidyl inositol-3 kinase (PI3 kinase),said method comprising selectively modulating the phosphatidylinositol-3 kinase (PI3 kinase) delta isoform over PI3 kinase betaisoform by administering an amount of a compound or pharmaceuticalcomposition to said subject, wherein said amount is sufficient forselective modulation of PI3 kinase delta isoform over PI3 kinase betaisoform.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.In case of conflict, the present application, including any definitionsherein, will control.

DETAILED DESCRIPTION

While specific embodiments of the present disclosure have beendiscussed, the specification is illustrative and not restrictive. Manyvariations of this disclosure will become apparent to those skilled inthe art upon review of this specification. The full scope of thedisclosure should be determined by reference to the claims, along withtheir full scope of equivalents, and the specification, along with suchvariations.

When ranges are used herein for physical properties, such as molecularweight, or chemical properties, such as chemical formulae, allcombinations and subcombinations of ranges and specific embodimentstherein are intended to be included. Unless otherwise indicated, allnumbers expressing quantities of ingredients, reaction conditions, andso forth used in the specification and claims are to be understood asbeing modified in all instances by the term “about.” The term “about”when referring to a number or a numerical range means that the number ornumerical range referred to is an approximation within experimentalvariability (or within statistical experimental error), and thus thenumber or numerical range can vary from, for example, but not limitedto, between 0.1% and 15% of the stated number or numerical range.Accordingly, unless indicated to the contrary, the numerical parametersset forth in this specification and attached claims are approximationsthat can vary depending upon the desired properties sought to beobtained by the present disclosure.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as is commonly understood by one of skill in theart to which this specification pertains.

As used in the specification and claims, the singular form “a”, “an” and“the” includes plural references unless the context clearly dictatesotherwise.

As used herein, “agent” or “biologically active agent” refers to abiological, pharmaceutical, or chemical compound or other moiety.Non-limiting examples include simple or complex organic or inorganicmolecules, a peptide, a protein, an oligonucleotide, an antibody, anantibody derivative, an antibody fragment, a vitamin, a vitaminderivative, a carbohydrate, a toxin, or a chemotherapeutic compound, andmetabolites thereof. Various compounds can be synthesized, for example,small molecules and oligomers (e.g., oligopeptides andoligonucleotides), and synthetic organic compounds based on various corestructures. In addition, various natural sources can provide compoundsfor screening, such as plant or animal extracts, and the like. A skilledartisan can readily recognize that there is no limit as to thestructural nature of the agents of this disclosure.

The term “agonist” as used herein refers to a compound or agent havingthe ability to initiate or enhance a biological function of a targetprotein or polypeptide, such as increasing the activity or expression ofthe target protein or polypeptide. Accordingly, the term “agonist” isdefined in the context of the biological role of the target protein orpolypeptide. While some agonists herein specifically interact with(e.g., bind to) the target, compounds and/or agents that initiate orenhance a biological activity of the target protein or polypeptide byinteracting with other members of the signal transduction pathway ofwhich the target polypeptide is a member are also specifically includedwithin this definition.

The terms “antagonist” and “inhibitor” are used interchangeably, andthey refer to a compound or agent having the ability to inhibit abiological function of a target protein or polypeptide, such as byinhibiting the activity or expression of the target protein orpolypeptide. Accordingly, the terms “antagonist” and “inhibitors” aredefined in the context of the biological role of the target protein orpolypeptide. While some antagonists herein specifically interact with(e.g., bind to) the target, compounds that inhibit a biological activityof the target protein or polypeptide by interacting with other membersof the signal transduction pathway of which the target protein orpolypeptide is a member are also specifically included within thisdefinition. Non-limiting examples of biological activity inhibited by anantagonist include those associated with the development, growth, orspread of a tumor, or an undesired immune response as manifested inautoimmune disease.

An “anti-cancer agent”, “anti-tumor agent” or “chemotherapeutic agent”refers to any agent useful in the treatment of a neoplastic condition.One class of anti-cancer agents comprises chemotherapeutic agents.“Chemotherapy” means the administration of one or more chemotherapeuticdrugs and/or other agents to a cancer patient by various methods,including intravenous, oral, intramuscular, intraperitoneal,intravesical, subcutaneous, transdermal, buccal, or inhalation or in theform of a suppository.

The term “cell proliferation” refers to a phenomenon by which the cellnumber has changed as a result of division. This term also encompassescell growth by which the cell morphology has changed (e.g., increased insize) consistent with a proliferative signal.

The term “co-administration,” “administered in combination with,” andtheir grammatical equivalents, as used herein, encompassesadministration of two or more agents to subject so that both agentsand/or their metabolites are present in the subject at the same time.Co-administration includes simultaneous administration in separatecompositions, administration at different times in separatecompositions, or administration in a composition in which both agentsare present.

The term “effective amount” or “therapeutically effective amount” refersto that amount of a compound or pharmaceutical composition describedherein that is sufficient to effect the intended application including,but not limited to, disease treatment, as illustrated below. Thetherapeutically effective amount can vary depending upon the intendedapplication (in vitro or in vivo), or the subject and disease conditionbeing treated, e.g., the weight and age of the subject, the severity ofthe disease condition, the manner of administration and the like, whichcan readily be determined by one of ordinary skill in the art. The termalso applies to a dose that will induce a particular response in targetcells, e.g., reduction of platelet adhesion and/or cell migration. Thespecific dose will vary depending on the particular compounds chosen,the dosing regimen to be followed, whether it is administered incombination with other agents, timing of administration, the tissue towhich it is administered, and the physical delivery system in which itis carried.

As used herein, the terms “treatment”, “treating”, “palliating” and“ameliorating” are used interchangeably herein. These terms refer to anapproach for obtaining beneficial or desired results including, but notlimited to, therapeutic benefit and/or a prophylactic benefit. Bytherapeutic benefit is meant eradication or amelioration of theunderlying disorder being treated. Also, a therapeutic benefit isachieved with the eradication or amelioration of one or more of thephysiological symptoms associated with the underlying disorder such thatan improvement is observed in the patient, notwithstanding that thepatient can still be afflicted with the underlying disorder. Forprophylactic benefit, the pharmaceutical compositions can beadministered to a patient at risk of developing a particular disease, orto a patient reporting one or more of the physiological symptoms of adisease, even though a diagnosis of this disease may not have been made.

A “therapeutic effect,” as that term is used herein, encompasses atherapeutic benefit and/or a prophylactic benefit as described above. Aprophylactic effect includes delaying or eliminating the appearance of adisease or condition, delaying or eliminating the onset of symptoms of adisease or condition, slowing, halting, or reversing the progression ofa disease or condition, or any combination thereof.

In certain embodiments, the pharmaceutically acceptable form thereof isa pharmaceutically acceptable salt. As used herein, the term“pharmaceutically acceptable salt” refers to those salts which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of subjects without undue toxicity, irritation,allergic response and the like, and are commensurate with a reasonablebenefit/risk ratio. Pharmaceutically acceptable salts are well known inthe art. For example, Berge et al. describes pharmaceutically acceptablesalts in detail in J. Pharmaceutical Sciences (1977) 66:1-19.Pharmaceutically acceptable salts of the compounds provided hereininclude those derived from suitable inorganic and organic acids andbases. Examples of pharmaceutically acceptable, nontoxic acid additionsalts are salts of an amino group formed with inorganic acids such ashydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid andperchloric acid or with organic acids such as acetic acid, oxalic acid,maleic acid, tartaric acid, citric acid, succinic acid or malonic acidor by using other methods used in the art such as ion exchange. Otherpharmaceutically acceptable salts include adipate, alginate, ascorbate,aspartate, benzenesulfonate, besylate, benzoate, bisulfate, borate,butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate,digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate,glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate,hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate,lactate, laurate, lauryl sulfate, malate, maleate, malonate,methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate,oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate,phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate,tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts,and the like. In some embodiments, organic acids from which salts can bederived include, for example, acetic acid, propionic acid, glycolicacid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinicacid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamicacid, mandelic acid, methanesulfonic acid, ethanesulfonic acid,p-toluenesulfonic acid, salicylic acid, and the like. Salts derived fromappropriate bases include alkali metal, alkaline earth metal, ammoniumand N+(C₁₋₄alkyl)⁴-salts. Representative alkali or alkaline earth metalsalts include sodium, lithium, potassium, calcium, magnesium, iron,zinc, copper, manganese, aluminum, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, lower alkyl sulfonate and aryl sulfonate. Organic bases fromwhich salts can be derived include, for example, primary, secondary, andtertiary amines, substituted amines including naturally occurringsubstituted amines, cyclic amines, basic ion exchange resins, and thelike, such as isopropylamine, trimethylamine, diethylamine,triethylamine, tripropylamine, and ethanolamine. In some embodiments,the pharmaceutically acceptable base addition salt is chosen fromammonium, potassium, sodium, calcium, and magnesium salts.

In certain embodiments, the pharmaceutically acceptable form thereof isa prodrug. As used herein, the term “prodrug” refers to compounds thatare transformed in vivo to yield a disclosed compound or apharmaceutically acceptable form of the compound. A prodrug can beinactive when administered to a subject, but is converted in vivo to anactive compound, for example, by hydrolysis (e.g., hydrolysis in blood).In certain cases, a prodrug has improved physical and/or deliveryproperties over the parent compound. Prodrugs are typically designed toenhance pharmaceutically and/or pharmacokinetically based propertiesassociated with the parent compound. The prodrug compound often offersadvantages of solubility, tissue compatibility or delayed release in amammalian organism (see, e.g., Bundgard, H., Design of Prodrugs (1985),pp. 7-9, 21-24 (Elsevier, Amsterdam). A discussion of prodrugs isprovided in Higuchi, T., et al., “Pro-drugs as Novel Delivery Systems,”A.C.S. Symposium Series, Vol. 14, and in Bioreversible Carriers in DrugDesign, ed. Edward B. Roche, American Pharmaceutical Association andPergamon Press, 1987, both of which are incorporated in full byreference herein. Exemplary advantages of a prodrug can include, but arenot limited to, its physical properties, such as enhanced watersolubility for parenteral administration at physiological pH compared tothe parent compound, or it enhances absorption from the digestive tract,or it can enhance drug stability for long-term storage.

The term “prodrug” is also meant to include any covalently bondedcarriers, which release the active compound in vivo when such prodrug isadministered to a subject. Prodrugs of an active compound, as describedherein, can be prepared by modifying functional groups present in theactive compound in such a way that the modifications are cleaved, eitherin routine manipulation or in vivo, to the parent active compound.Prodrugs include compounds wherein a hydroxy, amino or mercapto group isbonded to any group that, when the prodrug of the active compound isadministered to a subject, cleaves to form a free hydroxy, free amino orfree mercapto group, respectively. Examples of prodrugs include, but arenot limited to, acetate, formate and benzoate derivatives of an alcoholor acetamide, formamide and benzamide derivatives of an amine functionalgroup in the active compound and the like.

For example, if a disclosed compound or a pharmaceutically acceptableform of the compound contains a carboxylic acid functional group, aprodrug can comprise an ester formed by the replacement of the hydrogenatom of the acid group with a group such as (C₁-C₈)alkyl,(C₂-C₁₂)alkanoyloxymethyl, 1-(alkanoyloxy)ethyl having from 4 to 9carbon atoms, 1-methyl-1-(alkanoyloxy)-ethyl having from 5 to 10 carbonatoms, alkoxycarbonyloxymethyl having from 3 to 6 carbon atoms,1-(alkoxycarbonyloxy)ethyl having from 4 to 7 carbon atoms,1-methyl-1-(alkoxycarbonyloxy)ethyl having from 5 to 8 carbon atoms,N-(alkoxycarbonyl)aminomethyl having from 3 to 9 carbon atoms,1-(N-(alkoxycarbonyl)amino)ethyl having from 4 to 10 carbon atoms,3-phthalidyl, 4-crotonolactonyl, gamma-butyrolacton-4-yl,di-N,N—(C₁-C₂)alkylamino(C₂-C₃)alkyl (such as β-dimethylaminoethyl),carbamoyl-(C₁-C₂)alkyl, N,N-di(C₁-C₂)alkylcarbamoyl-(C₁-C₂)alkyl andpiperidino-, pyrrolidino- or morpholino(C₂-C₃)alkyl.

Similarly, if a disclosed compound or a pharmaceutically acceptable formof the compound contains an alcohol functional group, a prodrug can beformed by the replacement of the hydrogen atom of the alcohol group witha group such as (C₁-C₆)alkanoyloxymethyl, 1-((C₁-C₆)alkanoyloxy)ethyl,1-methyl-1-((C₁-C₆)alkanoyloxy)ethyl (C₁-C₆)alkoxycarbonyloxymethyl,N—(C₁-C₆)alkoxycarbonylaminomethyl, succinoyl, (C₁-C₆)alkanoyl,α-amino(C₁-C₄)alkanoyl, arylacyl and α-aminoacyl, orα-aminoacyl-α-aminoacyl, where each □-aminoacyl group is independentlyselected from the naturally occurring L-amino acids, P(O)(OH)₂,—P(O)(O(C₁-C₆)alkyl)₂ or glycosyl (the radical resulting from theremoval of a hydroxyl group of the hemiacetal form of a carbohydrate).

If a disclosed compound or a pharmaceutically acceptable form of thecompound incorporates an amine functional group, a prodrug can be formedby the replacement of a hydrogen atom in the amine group with a groupsuch as R-carbonyl, RO-carbonyl, NRR′-carbonyl where R and R′ are eachindependently (C₁-C₁₀)alkyl, (C₃-C₇)cycloalkyl, benzyl, or R-carbonyl isa natural α-aminoacyl or natural α-aminoacyl-natural α-aminoacyl,—C(OH)C(O)OY¹ wherein Y¹ is H, (C₁-C₆)alkyl or benzyl, —C(OY²)Y³ whereinY² is (C₁-C₄)alkyl and Y³ is (C₁-C₆)alkyl, carboxy(C₁-C₆)alkyl,amino(C₁-C₄)alkyl or mono-N— or di-N,N—(C₁-C₆)alkylaminoalkyl, —C(Y⁴)Y⁵wherein Y⁴ is H or methyl and Y⁵ is mono-N— or di-N,N—(C1-C6)alkylamino,morpholino, piperidin-1-yl or pyrrolidin-1-yl.

In certain embodiments, the pharmaceutically acceptable form thereof isa tautomer. As used herein, the term “tautomer” includes two or moreinterconvertable compounds resulting from at least one formal migrationof a hydrogen atom and at least one change in valency (e.g., a singlebond to a double bond, a triple bond to a single bond, or vice versa).“Tautomerization” includes prototropic or proton-shift tautomerization,which is considered a subset of acid-base chemistry. “Prototropictautomerization” or “proton-shift tautomerization” involves themigration of a proton accompanied by changes in bond order. The exactratio of the tautomers depends on several factors, includingtemperature, solvent, and pH. Where tautomerization is possible (e.g.,in solution), a chemical equilibrium of tautomers can be reached.Tautomerizations (i.e., the reaction providing a tautomeric pair) can becatalyzed by acid or base, or can occur without the action or presenceof an external agent. Exemplary tautomerizations include, but are notlimited to, keto-to-enol; amide-to-imide; lactam-to-lactim;enamine-to-imine; and enamine-to-(a different) enamine tautomerizations.A specific example of keto-enol tautomerization is the interconversionof pentane-2,4-dione and 4-hydroxypent-3-en-2-one tautomers. Anotherexample of tautomerization is phenol-keto tautomerization. A specificexample of phenol-keto tautomerization is the interconversion ofpyridin-4-ol and pyridin-4(1H)-one tautomers.

In certain embodiments, the pharmaceutically acceptable form thereof isan isomer. “Isomers” are different compounds that have the samemolecular formula. “Stereoisomers” are isomers that differ only in theway the atoms are arranged in space. As used herein, the term “isomer”includes any and all geometric isomers and stereoisomers. For example,“isomers” include cis- and trans-isomers, E- and Z-isomers, R- andS-enantiomers, diastereomers, (d)-isomers, (l)-isomers, racemic mixturesthereof, and other mixtures thereof, as falling within the scope of thisdisclosure. “Enantiomers” are a pair of stereoisomers that arenon-superimposable mirror images of each other. A mixture of a pair ofenantiomers in any proportion can be known as a “racemic” mixture. Theterm “(±)” is used to designate a racemic mixture where appropriate.“Diastereoisomers” are stereoisomers that have at least two asymmetricatoms, but which are not mirror-images of each other. The absolutestereochemistry is specified according to the Cahn-Ingold-Prelog R-Ssystem. When a compound is a pure enantiomer, the stereochemistry ateach chiral carbon can be specified by either R or S. Resolved compoundswhose absolute configuration is unknown can be designated (+) or (−)depending on the direction (dextro- or levorotatory) which they rotateplane polarized light at the wavelength of the sodium D line. Certain ofthe compounds described herein contain one or more asymmetric centersand can thus give rise to enantiomers, diastereomers, and otherstereoisomeric forms that can be defined, in terms of absolutestereochemistry, as (R)- or (S)-. The present chemical entities,pharmaceutical compositions and methods are meant to include all suchpossible isomers, including racemic mixtures, optically pure forms andintermediate mixtures. Optically active (R)- and (S)-isomers can beprepared, for example, using chiral synthons or chiral reagents, orresolved using conventional techniques. When the compounds describedherein contain olefinic double bonds or other centers of geometricasymmetry, and unless specified otherwise, it is intended that thecompounds include both E and Z geometric isomers.

The “enantiomeric excess” or “% enantiomeric excess” of a compositioncan be calculated using the equation shown below. In the example shownbelow, a composition contains 90% of one enantiomer, e.g., the Senantiomer, and 10% of the other enantiomer, e.g., the R enantiomer.

ee=(90−10)/100=80%.

Thus, a composition containing 90% of one enantiomer and 10% of theother enantiomer is said to have an enantiomeric excess of 80%. Some ofthe compositions described herein contain an enantiomeric excess of atleast about 50%, 75%, 90%, 95%, or 99% of Compound 1 (the S-enantiomer).In other words, the compositions contain an enantiomeric excess of the Senantiomer over the R enantiomer.

For instance, an isomer/enantiomer can, in some embodiments, be providedsubstantially free of the corresponding enantiomer, and can also bereferred to as “optically enriched.” “Optically-enriched,” as usedherein, means that the compound is made up of a significantly greaterproportion of one enantiomer. In certain embodiments, the compoundprovided herein is made up of at least about 90% by weight of oneenantiomer. In other embodiments the compound is made up of at leastabout 95%, 98%, or 99% by weight of one enantiomer. Enantiomers can beisolated from racemic mixtures by any method known to those skilled inthe art, including chiral high pressure liquid chromatography (HPLC),the formation and crystallization of chiral salts, or prepared byasymmetric syntheses. See, for example, Enantiomers, Racemates andResolutions (Jacques, Ed., Wiley Interscience, New York, 1981); Wilen etal., Tetrahedron 33:2725 (1977); Stereochemistry of Carbon Compounds (E.L. Eliel, Ed., McGraw-Hill, NY, 1962); and Tables of Resolving Agentsand Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of Notre DamePress, Notre Dame, Ind. 1972).

“Pharmaceutically acceptable carrier” or “pharmaceutically acceptableexcipient” includes any and all solvents, dispersion media, coatings,antibacterial and antifungal agents, isotonic and absorption delayingagents and the like. The use of such media and agents forpharmaceutically active substances is well known in the art. Exceptinsofar as any conventional media or agent is incompatible with theactive ingredient, its use in the therapeutic compositions as disclosedherein is contemplated. Supplementary active ingredients can also beincorporated into the pharmaceutical compositions.

“Signal transduction” is a process during which stimulatory orinhibitory signals are transmitted into and within a cell to elicit anintracellular response. A modulator of a signal transduction pathwayrefers to a compound which modulates the activity of one or morecellular proteins mapped to the same specific signal transductionpathway. A modulator can augment (agonist) or suppress (antagonist) theactivity of a signaling molecule.

The term “selective inhibition” or “selectively inhibit” as applied to abiologically active agent refers to the agent's ability to selectivelyreduce the target signaling activity as compared to off-target signalingactivity, via direct or interact interaction with the target. Forexample, a compound that selectively inhibits one isoform of PI3K overanother isoform of PI3K has an activity of at least 2× against a firstisoform relative to the compound's activity against the second isoform(e.g., at least 3×, 5×, 10×, 20×, 50×, or 100×).

The term “B-ALL” as used herein refers to B-cell Acute LymphoblasticLeukemia.

“Subject” to which administration is contemplated includes, but is notlimited to, humans (i.e., a male or female of any age group, e.g., apediatric subject (e.g., infant, child, adolescent) or adult subject(e.g., young adult, middle-aged adult or senior adult)) and/or otherprimates (e.g., cynomolgus monkeys, rhesus monkeys); mammals, includingcommercially relevant mammals such as cattle, pigs, horses, sheep,goats, cats, and/or dogs; and/or birds, including commercially relevantbirds such as chickens, ducks, geese, and/or turkeys.

“Radiation therapy” means exposing a patient, using routine methods andcompositions known to the practitioner, to radiation emitters such as,but not limited to, alpha-particle emitting radionuclides (e.g.,actinium and thorium radionuclides), low linear energy transfer (LET)radiation emitters (i.e., beta emitters), conversion electron emitters(e.g., strontium-89 and samarium-153-EDTMP, or high-energy radiation,including without limitation x-rays, gamma rays, and neutrons.

The term “in vivo” refers to an event that takes place in a subject'sbody.

The term “in vitro” refers to an event that takes places outside of asubject's body. For example, an in vitro assay encompasses any assayconducted outside of a subject. In vitro assays encompass cell-basedassays in which cells, alive or dead, are employed. In vitro assays alsoencompass a cell-free assay in which no intact cells are employed.

Unless otherwise stated, structures depicted herein are also meant toinclude compounds which differ only in the presence of one or moreisotopically enriched atoms. For example, compounds having the presentstructures except for the replacement of a hydrogen by a deuterium ortritium, or the replacement of a carbon by ¹³C— or ¹⁴C-enriched carbonare within the scope of this disclosure.

The disclosure also embraces isotopically labeled compounds which areidentical to those recited herein, except that one or more atoms arereplaced by an atom having an atomic mass or mass number different fromthe atomic mass or mass number usually found in nature. Examples ofisotopes that can be incorporated into disclosed compounds includeisotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, fluorine andchlorine, such as ²H, ³H, ¹³C, ¹⁴C, ¹⁵N, ¹⁸O, ¹⁷O, ³¹P, ³²P, ³⁵S, ¹⁸F,and ³⁶Cl, respectively. Certain isotopically-labeled disclosed compounds(e.g., those labeled with ³H and ¹⁴C) are useful in compound and/orsubstrate tissue distribution assays. Tritiated (i.e., ³H) and carbon-14(i.e., ¹⁴C) isotopes can allow for ease of preparation anddetectability. Further, substitution with heavier isotopes such asdeuterium (i.e., ²H) can afford certain therapeutic advantages resultingfrom greater metabolic stability (e.g., increased in vivo half-life orreduced dosage requirements). Isotopically labeled disclosed compoundscan generally be prepared by substituting an isotopically labeledreagent for a non-isotopically labeled reagent. In some embodiments,provided herein are compounds that can also contain unnaturalproportions of atomic isotopes at one or more of atoms that constitutesuch compounds. All isotopic variations of the compounds as disclosedherein, whether radioactive or not, are encompassed within the scope ofthe present disclosure.

The following abbreviations and terms have the indicated meaningsthroughout: PI3K=Phosphoinositide 3-kinase; PI=phosphatidylinositol;PDK=Phosphoinositide Dependent Kinase; DNA-PK=Deoxyribose Nucleic AcidDependent Protein Kinase; PTEN=Phosphatase and Tensin homolog deleted onchromosome Ten; PIKK=Phosphoinositide Kinase Like Kinase; AIDS=AcquiredImmuno Deficiency Syndrome; HIV=Human Immunodeficiency Virus; MeI=MethylIodide; POCl₃=Phosphorous Oxychloride; KCNS=Potassium Isothiocyanate;TLC=Thin Layer Chromatography; MeOH=Methanol; and CHCl₃=Chloroform.

“Alkyl” refers to a straight or branched hydrocarbon chain radicalconsisting solely of carbon and hydrogen atoms, containing nounsaturation, having from one to ten carbon atoms (e.g., C₁-C₁₀ alkyl).Whenever it appears herein, a numerical range such as “1 to 10” refersto each integer in the given range; e.g., “1 to 10 carbon atoms” meansthat the alkyl group can consist of 1 carbon atom, 2 carbon atoms, 3carbon atoms, etc., up to and including 10 carbon atoms, although thepresent definition also covers the occurrence of the term “alkyl” whereno numerical range is designated. In some embodiments, it is a C₁-C₆alkyl group. Typical alkyl groups include, but are in no way limited to,methyl, ethyl, propyl, isopropyl, n-butyl, iso-butyl, sec-butylisobutyl, tertiary butyl, pentyl, isopentyl, neopentyl, hexyl, septyl,octyl, nonyl, decyl, and the like. The alkyl is attached to the rest ofthe molecule by a single bond, for example, methyl (Me), ethyl (Et),n-propyl, 1-methylethyl (iso-propyl), n-butyl, n-pentyl,1,1-dimethylethyl (t-butyl), 3-methylhexyl, 2-methylhexyl, and the like.Unless stated otherwise specifically in the specification, an alkylgroup is optionally substituted by one or more of substituents whichindependently include: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy,halo, cyano, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl,—OR^(a), —SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(s))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(s))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂ whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Alkylaryl” refers to an -(alkyl)aryl radical where aryl and alkyl areas disclosed herein and which are optionally substituted by one or moreof the substituents described as suitable substituents for aryl andalkyl respectively. The “alkylaryl” is bonded to the parent molecularstructure through the alkyl group.

“Alkylheteroaryl” refers to an -(alkyl)heteroaryl radical whereheteroaryl and alkyl are as disclosed herein and which are optionallysubstituted by one or more of the substituents described as suitablesubstituents for aryl and alkyl respectively. The “alkylheteroaryl” isbonded to the parent molecular structure through the alkyl group.

“Alkylheterocycloalkyl” refers to an -(alkyl) heterocycyl radical wherealkyl and heterocycloalkyl are as disclosed herein and which areoptionally substituted by one or more of the substituents described assuitable substituents for heterocycloalkyl and alkyl respectively. The“alkylheterocycloalkyl” is bonded to the parent molecular structurethrough the alkyl group.

“Alkenyl” refers to a straight or branched hydrocarbon chain radicalgroup consisting solely of carbon and hydrogen atoms, containing atleast one double bond, and having from two to ten carbon atoms (i.e.,C₂-C₁₀ alkenyl). Whenever it appears herein, a numerical range such as“2 to 10” refers to each integer in the given range; e.g., “2 to 10carbon atoms” means that the alkenyl group can consist of 2 carbonatoms, 3 carbon atoms, etc., up to and including 10 carbon atoms. Incertain embodiments, an alkenyl comprises two to eight carbon atoms. Inother embodiments, an alkenyl comprises two to five carbon atoms (e.g.,C₂-C₅ alkenyl). The alkenyl is attached to the parent molecularstructure by a single bond, for example, ethenyl (i.e., vinyl),prop-1-enyl (i.e., allyl), but-1-enyl, pent-1-enyl, penta-1,4-dienyl,and the like. Unless stated otherwise specifically in the specification,an alkenyl group is optionally substituted by one or more substituentswhich independently include: alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, trifluoromethyl,trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a), —SR^(a),—OC(O)—R^(a), —N(R^(a))², —C(O)R^(a), —C(O)OR^(a), —OC(O)N(R^(a))²,—C(O)N(R^(a))², —N(R^(a))C(O)OR^(a), —N(R^(a))C(O)R^(a),—N(R^(a))C(O)N(R^(a))², N(R^(a))C(NR^(a))N(R^(a))²,—N(R^(a))S(O)_(t)R_(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))² (where t is 1 or 2), or PO₃(R^(a))², whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Alkenyl-cycloalkyl” refers to an -(alkenyl)cycloalkyl radical wherealkenyl and cyclo alkyl are as disclosed herein and which are optionallysubstituted by one or more of the substituents described as suitablesubstituents for alkenyl and cycloalkyl respectively. The“alkenyl-cycloalkyl” is bonded to the parent molecular structure throughthe alkenyl group.

“Alkynyl” refers to a straight or branched hydrocarbon chain radicalgroup consisting solely of carbon and hydrogen atoms, containing atleast one triple bond, having from two to ten carbon atoms (i.e., C₂-C₁₀alkynyl). Whenever it appears herein, a numerical range such as “2 to10” refers to each integer in the given range; e.g., “2 to 10 carbonatoms” means that the alkynyl group can consist of 2 carbon atoms, 3carbon atoms, etc., up to and including 10 carbon atoms. In certainembodiments, an alkynyl comprises two to eight carbon atoms. In otherembodiments, an alkynyl has two to five carbon atoms (e.g., C₂-C₅alkynyl). The alkynyl is attached to the parent molecular structure by asingle bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl,and the like. Unless stated otherwise specifically in the specification,an alkynyl group is optionally substituted by one or more substituentswhich independently include: alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, trifluoromethyl,trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a), —SR^(a),—OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a), —OC(O)N(R^(a))₂,—C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a), —N(R^(a))C(O)R^(a),—N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Alkynyl-cycloalkyl” refers to refers to an -(alkynyl)cycloalkyl radicalwhere alkynyl and cycloalkyl are as disclosed herein and which areoptionally substituted by one or more of the substituents described assuitable substituents for alkynyl and cycloalkyl respectively. The“alkynyl-cycloalkyl” is bonded to the parent molecular structure throughthe alkenyl group.

“Carboxaldehyde” refers to a —(C═O)H radical.

“Carboxyl” refers to a —(C═O)OH radical.

“Cyano” refers to a —CN radical.

“Cycloalkyl” refers to a monocyclic or polycyclic radical that containsonly carbon and hydrogen, and can be saturated, or partiallyunsaturated. Cycloalkyl groups include groups having from 3 to 10 ringatoms (i.e., C₃-C₁₀ cycloalkyl). Whenever it appears herein, a numericalrange such as “3 to 10” refers to each integer in the given range; e.g.,“3 to 10 carbon atoms” means that the cycloalkyl group can consist of 3carbon atoms, 4 carbon atoms, 5 carbon atoms, etc., up to and including10 carbon atoms. In some embodiments, it is a C₃-C₈ cycloalkyl radical.In some embodiments, it is a C₃-C₅ cycloalkyl radical. Illustrativeexamples of cycloalkyl groups include, but are not limited to thefollowing moieties: cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl,cyclohexyl, cyclohexenyl, cycloseptyl, cyclooctyl, cyclononyl,cyclodecyl, norbornyl, and the like. The term “cycloalkyl” also includesbridged and spiro-fused cyclic structures containing no heteroatoms. Theterm also includes monocyclic or fused-ring polycyclic (i.e., ringswhich share adjacent pairs of ring atoms) groups. Unless statedotherwise specifically in the specification, a cycloalkyl group isoptionally substituted by one or more substituents which independentlyinclude: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy,halo, cyano, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl,—OR^(a), —SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Cycloalkyl-alkenyl” refers to a -(cycloalkyl)alkenyl radical wherecycloalkyl and heterocycloalkyl are as disclosed herein and which areoptionally substituted by one or more of the substituents described assuitable substituents for heterocycloalkyl and cycloalkyl respectively.The “cycloalkyl-alkenyl” is bonded to the parent molecular structurethrough the cycloalkyl group.

“Cycloalkyl-heterocycloalkyl” refers to a -(cycloalkyl) heterocycylradical where cycloalkyl and heterocycloalkyl are as disclosed hereinand which are optionally substituted by one or more of the substituentsdescribed as suitable substituents for heterocycloalkyl and cycloalkylrespectively. The “cycloalkyl-heterocycloalkyl” is bonded to the parentmolecular structure through the cycloalkyl group.

“Cycloalkyl-heteroaryl” refers to a -(cycloalkyl) heteroaryl radicalwhere cycloalkyl and heterocycloalkyl are as disclosed herein and whichare optionally substituted by one or more of the substituents describedas suitable substituents for heterocycloalkyl and cycloalkylrespectively. The “cycloalkyl-heteroaryl” is bonded to the parentmolecular structure through the cycloalkyl group.

The term “alkoxy” refers to the group —O-alkyl, including from 1 to 10carbon atoms of a straight, branched, cyclic configuration andcombinations thereof, attached to the parent molecular structure throughan oxygen. Examples include methoxy, ethoxy, propoxy, isopropoxy,cyclopropyloxy, cyclohexyloxy and the like. “Lower alkoxy” refers toalkoxy groups containing one to six carbons. In some embodiments, C₁-C₄alkyl is an alkyl group which encompasses both straight and branchedchain alkyls of from 1 to 4 carbon atoms.

The term “substituted alkoxy” refers to alkoxy wherein the alkylconstituent is substituted (i.e., —O-(substituted alkyl)). Unless statedotherwise specifically in the specification, the alkyl moiety of analkoxy group is optionally substituted by one or more substituents whichindependently include: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy,halo, cyano, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl,—OR^(a), SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

The term “alkoxycarbonyl” refers to a group of the formula(alkoxy)(C═O)— attached to the parent molecular structure through thecarbonyl carbon wherein the alkoxy group has the indicated number ofcarbon atoms. Thus a C₁-C₆ alkoxycarbonyl group is an alkoxy grouphaving from 1 to 6 carbon atoms attached through its oxygen to acarbonyl linker. “Lower alkoxycarbonyl” refers to an alkoxycarbonylgroup wherein the alkyl portion of the alkoxy group is a lower alkylgroup. In some embodiments, C₁-C₄ alkoxy, is an alkoxy group whichencompasses both straight and branched chain alkoxy groups of from 1 to4 carbon atoms.

The term “substituted alkoxycarbonyl” refers to the group (substitutedalkyl)-O—C(O)— wherein the group is attached to the parent molecularstructure through the carbonyl functionality. Unless stated otherwisespecifically in the specification, the alkyl moiety of an alkoxycarbonylgroup is optionally substituted by one or more substituents whichindependently include: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy,halo, cyano, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl,—OR^(a), SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))C(O)N(R^(a))_(2i)N(R^(a))C(NR^(a))N(R^(a))₂, —N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2),—S(O)_(t)OR^(a) (where t is 1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or2), or PO₃(R^(a))₂, where each R^(a) is independently hydrogen, alkyl,fluoroalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl,heterocycloalkyl, heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Acyl” refers to R—C(O)— groups such as (alkyl)-C(O)—, (aryl)-C(O)—,(heteroaryl)-C(O)—, (heteroalkyl)-C(O)—, and (heterocycloalkyl)-C(O)—,wherein the group is attached to the parent molecular structure throughthe carbonyl functionality. In some embodiments, it is a C₁-C₁₀ acylradical which refers to the total number of chain or ring atoms of thealkyl, aryl, heteroaryl or heterocycloalkyl portion of the alkyl groupplus the carbonyl carbon of acyl, i.e., a C₄-acyl has three other ringor chain atoms plus carbonyl. If the R radical is heteroaryl orheterocycloalkyl, the hetero ring or chain atoms contribute to the totalnumber of chain or ring atoms. Unless stated otherwise specifically inthe specification, the “R” of an acyloxy group is optionally substitutedby one or more substituents which independently include: alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,arylalkyl, heteroaryl, heteroarylalkyl, hydroxy, halo, cyano,trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a),SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Acyloxy” refers to a R(C═O)O— radical wherein “R” is alkyl, aryl,heteroaryl, heteroalkyl, or heterocycloalkyl, which are as describedherein. In some embodiments, it is a C₁-C₄ acyloxy radical which refersto the total number of chain or ring atoms of the alkyl, aryl,heteroaryl or heterocycloalkyl portion of the acyloxy group plus thecarbonyl carbon of acyl, i.e., a C₄-acyloxy has three other ring orchain atoms plus carbonyl. If the R radical is heteroaryl orheterocycloalkyl, the hetero ring or chain atoms contribute to the totalnumber of chain or ring atoms. Unless stated otherwise specifically inthe specification, the “R” of an acyloxy group is optionally substitutedby one or more substituents which independently include: alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,arylalkyl, heteroaryl, heteroarylalkyl, hydroxy, halo, cyano,trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a),—SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2-S(O)_(t)OR^(a) (where t is 1or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Amino” or “amine” refers to a —N(R^(a))₂ radical group, where eachR^(a) is independently hydrogen, alkyl, haloalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl, unless statedotherwise specifically in the specification. When a —N(R^(a))₂ group hastwo R^(a) other than hydrogen, they can be combined with the nitrogenatom to form a 4-, 5-, 6-, or 7-membered ring. For example, —N(R^(a))₂is meant to include, but not be limited to, 1-pyrrolidinyl and4-morpholinyl. Unless stated otherwise specifically in thespecification, an amino group is optionally substituted by one or moresubstituents which independently include: alkyl, heteroalkyl, alkenyl,alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, trifluoromethyl,trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a), —SR^(a),—OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a), —OC(O)N(R^(a))₂,—C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a), —N(R^(a))C(O)]R^(a),—N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl and each of thesemoieties can be optionally substituted as defined herein.

The term “substituted amino” also refers to N-oxides of the groups—N⁺(H)(R^(a))O⁻, and —N⁺(R^(a))(R^(a))O⁻, R^(a) as described above,where the N-oxide is bonded to the parent molecular structure throughthe N atom. N-oxides can be prepared by treatment of the correspondingamino group with, for example, hydrogen peroxide orm-chloroperoxybenzoic acid. The person skilled in the art is familiarwith reaction conditions for carrying out the N-oxidation.

“Amide” or “amido” refers to a chemical moiety with formula —C(O)N(R)₂or —NRC(O)R, where R is selected from hydrogen, alkyl, cycloalkyl, aryl,heteroaryl (bonded through a ring carbon) and heteroalicyclic (bondedthrough a ring carbon), each of which moiety can itself be optionallysubstituted. In some embodiments it is a C₁-C₄ amido or amide radical,which includes the amide carbonyl in the total number of carbons in theradical. The R₂ of —N(R)₂ of the amide can optionally be taken togetherwith the nitrogen to which it is attached to form a 4-, 5-, 6-, or7-membered ring. Unless stated otherwise specifically in thespecification, an amido group is optionally substituted independently byone or more of the substituents as described herein for alkyl,cycloalkyl, aryl, heteroaryl, or heterocycloalkyl. An amide can be anamino acid or a peptide molecule attached to a compound of Formula (I),thereby forming a prodrug. Any amine, hydroxy, or carboxyl side chain onthe compounds described herein can be transformed into an amide group.The procedures and specific groups to make such amides are known tothose of skill in the art and can readily be found in reference sourcessuch as Greene and Wuts, Protective Groups in Organic Synthesis, 3rdEd., John Wiley & Sons, New York, N.Y., 1999, which is incorporatedherein by reference in its entirety.

“Aromatic” or “aryl” refers to a radical with six to ten ring atoms(e.g., C₆-C₁₀ aromatic or C₆-C₁₀ aryl) which has at least one ringhaving a conjugated pi electron system which is carbocyclic (e.g.,phenyl, fluorenyl, and naphthyl). Bivalent radicals formed fromsubstituted benzene derivatives and having the free valences at ringatoms are named as substituted phenylene radicals. Bivalent radicalsderived from univalent polycyclic hydrocarbon radicals whose names endin “-yl” by removal of one hydrogen atom from the carbon atom with thefree valence are named by adding “-idene” to the name of thecorresponding univalent radical, e.g., a naphthyl group with two pointsof attachment is termed naphthylidene. Whenever it appears herein, anumerical range such as “6 to 10” refers to each integer in the givenrange; e.g., “6 to 10 ring atoms” means that the aryl group can consistof 6 ring atoms, 7 ring atoms, etc., up to and including 10 ring atoms.The term includes monocyclic or fused-ring polycyclic (i.e., rings whichshare adjacent pairs of ring atoms) groups. Unless stated otherwisespecifically in the specification, an aryl moiety can be optionallysubstituted by one or more substituents which are independently: alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,arylalkyl, heteroaryl, heteroarylalkyl, hydroxy, halo, cyano,trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a),—SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)]R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Aralkyl” or “arylalkyl” refers to an (aryl)alkyl-radical where aryl andalkyl are as disclosed herein and which are optionally substituted byone or more of the substituents described as suitable substituents foraryl and alkyl respectively. The “aralkyl/arylalkyl” is bonded to theparent molecular structure through the alkyl group.

As used herein, a “covalent bond” or “direct bond” refers to a singlebond joining two groups.

“Ester” refers to a chemical radical of formula —COOR, where R isselected from alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ringcarbon) and heteroalicyclic (bonded through a ring carbon). Any amine,hydroxy, or carboxyl side chain on the compounds described herein can beesterified. The procedures and specific groups to make such esters areknown to those of skill in the art and can readily be found in referencesources such as Greene and Wuts, Protective Groups in Organic Synthesis,3rd Ed., John Wiley & Sons, New York, N.Y., 1999, which is incorporatedherein by reference in its entirety. Unless stated otherwisespecifically in the specification, an ester group can be optionallysubstituted by one or more substituents which independently are: alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,arylalkyl, heteroaryl, heteroarylalkyl, hydroxy, halo, cyano,trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a),—SR^(a), —OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a),—OC(O)N(R^(a))₂, —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)]R^(a), —N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂, whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Fluoroalkyl” refers to an alkyl radical, as defined above, that issubstituted by one or more fluoro radicals, as defined above, forexample, trifluoromethyl, difluoromethyl, 2,2,2-trifluoroethyl,1-fluoromethyl-2-fluoroethyl, and the like. The alkyl part of thefluoroalkyl radical can be optionally substituted as defined above foran alkyl group.

“Halo”, “halide”, or, alternatively, “halogen” means fluoro, chloro,bromo or iodo. The terms “haloalkyl,” “haloalkenyl,” “haloalkynyl” and“haloalkoxy” include alkyl, alkenyl, alkynyl and alkoxy structures thatare substituted with one or more halo groups or with combinationsthereof. For example, the terms “fluoroalkyl” and “fluoroalkoxy” includehaloalkyl and haloalkoxy groups, respectively, in which the halo isfluorine.

“Heteroalkyl” “heteroalkenyl” and “heteroalkynyl” include optionallysubstituted alkyl, alkenyl and alkynyl radicals and which have one ormore skeletal chain atoms selected from an atom other than carbon, e.g.,oxygen, nitrogen, sulfur, phosphorus or combinations thereof. Anumerical range can be given, e.g., C₁-C₄ heteroalkyl which refers tothe chain length in total, which in this example is 4 atoms long. Forexample, a —CH₂OCH₂CH₃ radical is referred to as a “C₄” heteroalkyl,which includes the heteroatom center in the atom chain lengthdescription. Connection to the rest of the parent molecular structurecan be through either a heteroatom or a carbon in the heteroalkyl chain.A heteroalkyl group can be substituted with one or more substituentswhich independently are: alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, nitro, oxo, thioxo,trimethylsilanyl, —OR^(a), —SR^(a), —OC(O)—R^(a), —N(R^(a))₂,—C(O)R^(a), —C(O)OR^(a), —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)R^(a), —N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2),—S(O)_(t)OR^(a) (where t is 1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or2), or PO₃(R^(a))₂, where each R^(a) is independently hydrogen, alkyl,fluoroalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl,heterocycloalkyl, heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

“Heteroalkylaryl” refers to an -(heteroalkyl)aryl radical whereheteroalkyl and aryl are as disclosed herein and which are optionallysubstituted by one or more of the substituents described as suitablesubstituents for heteroalkyl and aryl respectively. The“heteroalkylaryl” is bonded to the parent molecular structure through acarbon atom of the heteroalkyl group.

“Heteroalkylheteroaryl” refers to an -(heteroalkyl)heteroaryl radicalwhere heteroalkyl and heteroaryl are as disclosed herein and which areoptionally substituted by one or more of the substituents described assuitable substituents for heteroalkyl and heteroaryl respectively. The“heteroalkylheteroaryl” is bonded to the parent molecular structurethrough a carbon atom of the heteroalkyl group.

“Heteroalkylheterocycloalkyl” refers to an-(heteroalkyl)heterocycloalkyl radical where heteroalkyl and heteroarylare as disclosed herein and which are optionally substituted by one ormore of the substituents described as suitable substituents forheteroalkyl and heterocycloalkyl respectively. The“heteroalkylheterocycloalkyl” is bonded to the parent molecularstructure through a carbon atom of the heteroalkyl group.

“Heteroalkylcycloalkyl” refers to an -(heteroalkyl)cycloalkyl radicalwhere heteroalkyl and cycloalkyl are as disclosed herein and which areoptionally substituted by one or more of the substituents described assuitable substituents for heteroalkyl and cycloalkyl respectively. The“heteroalkylcycloalkyl” is bonded to the parent molecular structurethrough a carbon atom of the heteroalkyl group.

“Heteroaryl” or, alternatively, “heteroaromatic” refers to a 5- to18-membered aromatic radical (e.g., C₅-C₁₃ heteroaryl) that includes oneor more ring heteroatoms selected from nitrogen, oxygen and sulfur, andwhich can be a monocyclic, bicyclic, tricyclic or tetracyclic ringsystem. Whenever it appears herein, a numerical range such as “5 to 18”refers to each integer in the given range; e.g., “5 to 18 ring atoms”means that the heteroaryl group can consist of 5 ring atoms, 6 ringatoms, etc., up to and including 18 ring atoms. Bivalent radicalsderived from univalent heteroaryl radicals whose names end in “-yl” byremoval of one hydrogen atom from the atom with the free valence arenamed by adding “-idene” to the name of the corresponding univalentradical, e.g., a pyridyl group with two points of attachment is apyridylidene. An N-containing “heteroaromatic” or “heteroaryl” moietyrefers to an aromatic group in which at least one of the skeletal atomsof the ring is a nitrogen atom. The polycyclic heteroaryl group can befused or non-fused. The heteroatom(s) in the heteroaryl radical isoptionally oxidized. One or more nitrogen atoms, if present, areoptionally quaternized. The heteroaryl is attached to the parentmolecular structure through any atom of the ring(s). Examples ofheteroaryls include, but are not limited to, azepinyl, acridinyl,benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzofuranyl,benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl,benzo[b][1,4]dioxepinyl, benzo[b][1,4]oxazinyl, 1,4-benzodioxanyl,benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl,benzoxazolyl, benzopyranyl, benzopyranonyl, benzofuranyl,benzofuranonyl, benzofurazanyl, benzothiazolyl, benzothienyl(benzothiophenyl), benzothieno[3,2-d]pyrimidinyl, benzotriazolyl,benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl,cyclopenta[d]pyrimidinyl,6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidinyl,5,6-dihydrobenzo[h]quinazolinyl, 5,6-dihydrobenzo[h]cinnolinyl,6,7-dihydro-5H-benzo[6,7]cyclohepta[1,2-c]pyridazinyl, dibenzofuranyl,dibenzothiophenyl, furanyl, furazanyl, furanonyl, furo[3,2-c]pyridinyl,5,6,7,8,9,10-hexahydrocycloocta[d]pyrimidinyl,5,6,7,8,9,10-hexahydrocycloocta[d]pyridazinyl,5,6,7,8,9,10-hexahydrocycloocta[d]pyridinyl, isothiazolyl, imidazolyl,indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl,isoquinolyl, indolizinyl, isoxazolyl,5,8-methano-5,6,7,8-tetrahydroquinazolinyl, naphthyridinyl,1,6-naphthyridinonyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl,5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazolinyl, 1-phenyl-1H-pyrrolyl,phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl,purinyl, pyranyl, pyrrolyl, pyrazolyl, pyrazolo[3,4-d]pyrimidinyl,pyridinyl, pyrido[3,2-d]pyrimidinyl, pyrido[3,4-d]pyrimidinyl,pyrazinyl, pyrimidinyl, pyridazinyl, pyrrolyl, quinazolinyl,quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl,5,6,7,8-tetrahydroquinazolinyl,5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinyl,6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidinyl,5,6,7,8-tetrahydropyrido[4,5-c]pyridazinyl, thiazolyl, thiadiazolyl,thiapyranyl, triazolyl, tetrazolyl, triazinyl, thieno[2,3-d]pyrimidinyl,thieno[3,2-d]pyrimidinyl, thieno[2,3-c]pridinyl, and thiophenyl (i.e.,thienyl). Unless stated otherwise specifically in the specification, aheteroaryl moiety is optionally substituted by one or more substituentswhich are independently: alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, nitro, oxo, thioxo,trimethylsilanyl, —OR^(a), —SR^(a), —OC(O)—R^(a), —N(R^(a))₂,—C(O)R^(a), —C(O)OR^(a), —C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a),—N(R^(a))C(O)]R^(a), —N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2),—S(O)_(t)OR^(a) (where t is 1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or2), or PO₃(R^(a))₂, where each R^(a) is independently hydrogen, alkyl,fluoroalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl,heterocycloalkyl, heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

Substituted heteroaryl also includes ring systems substituted with oneor more oxide (—O—) substituents, such as pyridinyl N-oxides.

“Heterocyclyl” refers to any 3- to 18-membered aromatic radicalmonocyclic or polycyclic moiety comprising at least one heteroatomselected from nitrogen, oxygen and sulfur. As used herein, heterocyclylmoieties can be aromatic or nonaromatic. A heterocyclyl group can be amonocyclic, bicyclic, tricyclic or tetracyclic ring system. Whenever itappears herein, a numerical range such as “3 to 18” refers to eachinteger in the given range; e.g., “5 to 18 ring atoms” means that theheterocyclyl group can consist of 5 ring atoms, 6 ring atoms, etc., upto and including 18 ring atoms. Bivalent radicals derived from univalentheterocyclyl radicals whose names end in “-yl” by removal of onehydrogen atom from the atom with the free valence are named by adding“-idene” to the name of the corresponding univalent radical, e.g., apiperidine group with two points of attachment is a piperidylidene. AnN-containing heterocyclyl moiety refers to an non-aromatic group inwhich at least one of the skeletal atoms of the ring is a nitrogen atom.The polycyclic heterocyclyl group can be fused or non-fused. Theheteroatom(s) in the heterocyclyl radical is optionally oxidized. One ormore nitrogen atoms, if present, are optionally quaternized. Theheteroaryl is attached to the parent molecular structure through anyatom of the ring(s). Unless stated otherwise, heterocyclyl moieties areoptionally substituted by one or more substituents which independentlyare: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl,aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy, halo, cyano,nitro, oxo, thioxo, trimethylsilanyl, —OR^(a), —SR^(a), —OC(O)—R^(a),—N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a), —C(O)N(R^(a))₂,—N(R^(a))C(O)OR^(a), —N(R^(a))C(O)R^(a), —N(R^(a))S(O)_(t)R^(a) (where tis 1 or 2), —S(O)_(t)OR^(a) (where t is 1 or 2), —S(O)_(t)N(R^(a))₂(where t is 1 or 2), or PO₃(R^(a))₂, where each R^(a) is independentlyhydrogen, alkyl, fluoroalkyl, carbocyclyl, carbocyclylalkyl, aryl,aralkyl, heterocycloalkyl, heteroaryl or heteroarylalkyl.

“Heteroarylalkyl” refers to an -(heteroaryl) alkyl radical whereheteroaryl and alkyl are as disclosed herein and which are optionallysubstituted by one or more of the substituents described as suitablesubstituents for heteroaryl and alkyl respectively. The“heteroarylalkyl” is bonded to the parent molecular structure throughany atom of the heteroaryl group.

“Heterocycloalkyl” refers to a stable 3- to 18-membered non-aromaticring radical that comprises two to twelve carbon atoms and from one tosix heteroatoms selected from nitrogen, oxygen and sulfur. Whenever itappears herein, a numerical range such as “3 to 18” refers to eachinteger in the given range; e.g., “3 to 18 ring atoms” means that theheterocycloalkyl group can consist of 3 ring atoms, 4 ring atoms, etc.,up to and including 18 ring atoms. In some embodiments, it is a C₅-C₁₀heterocycloalkyl. In some embodiments, it is a C₄-C₁₀ heterocycloalkyl.In some embodiments, it is a C₃-C₁₀ heterocycloalkyl. Unless statedotherwise specifically in the specification, the heterocycloalkylradical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system,which can include fused or bridged ring systems. The heteroatoms in theheterocycloalkyl radical can be optionally oxidized. One or morenitrogen atoms, if present, are optionally quaternized. Theheterocycloalkyl radical is partially or fully saturated. Theheterocycloalkyl can be attached to the parent molecular group throughany atom of the ring(s). Examples of such heterocycloalkyl radicalsinclude, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl,decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl,isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl,2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl,piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl,quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl,tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl,1-oxo-thiomorpholinyl, and 1,1-dioxo-thiomorpholinyl. Unless statedotherwise specifically in the specification, a heterocycloalkyl moietyis optionally substituted by one or more substituents whichindependently include: alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, hydroxy,halo, cyano, nitro, oxo, thioxo, trimethylsilanyl, —OR^(a), —SR^(a),—OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a), —C(O)N(R^(a))₂,—N(R^(a))C(O)OR^(a), —N(R^(a))C(O)R^(a), —N(R^(a))S(O)_(t)R^(a) (where tis 1 or 2), —S(O)_(t)OR^(a) (where t is 1 or 2), —S(O)_(t)N(R^(a))₂(where t is 1 or 2), or PO₃(R^(a))₂, where each R^(a) is independentlyhydrogen, alkyl, fluoroalkyl, carbocyclyl, carbocyclylalkyl, aryl,aralkyl, heterocycloalkyl, heteroaryl or heteroarylalkyl.

“Heterocycloalkyl” also includes bicyclic ring systems wherein onenon-aromatic ring, such as a ring having 3 to 7 ring atoms, contains atleast 2 carbon atoms in addition to 1-3 heteroatoms independentlyselected from oxygen, sulfur, and nitrogen, as well as combinationscomprising at least one of the foregoing heteroatoms; and the otherring, usually having 3 to 7 ring atoms, optionally contains 1-3heteroatoms independently selected from oxygen, sulfur, and nitrogen andis not aromatic.

“Moiety” refers to a specific segment or functional group of a molecule.Chemical moieties are often recognized chemical entities embedded in orappended to a molecule.

“Nitro” refers to the —NO₂ radical.

“Oxa” refers to the —O— radical.

“Oxo” refers to the ═O radical.

A “leaving group or atom” is any group or atom that will, under thereaction conditions, cleave from the starting material, thus promotingreaction at a specified site. Suitable non-limiting examples of suchgroups unless otherwise specified include halogen atoms, mesyloxy,p-nitrobenzensulphonyloxy and tosyloxy groups.

“Protecting group” has the meaning conventionally associated with it inorganic synthesis, i.e., a group that selectively blocks one or morereactive sites in a multifunctional compound such that a chemicalreaction can be carried out selectively on another unprotected reactivesite and such that the group can readily be removed after the selectivereaction is complete. A variety of protecting groups are disclosed, forexample, in T. H. Greene and P. G. M. Wuts, Protective Groups in OrganicSynthesis, Third Edition, John Wiley & Sons, New York (1999). Forexample, a hydroxy protected form is where at least one of the hydroxygroups present in a compound is protected with a hydroxy protectinggroup. Likewise, amines and other reactive groups can similarly beprotected.

“Substituted” means that the referenced group can be substituted withone or more additional group(s) individually and independently selectedfrom acyl, alkyl, alkylaryl, cycloalkyl, aralkyl, aryl, carbohydrate,carbonate, heteroaryl, heterocycloalkyl, hydroxy, alkoxy, aryloxy,mercapto, alkylthio, arylthio, cyano, halo, carbonyl, ester,thiocarbonyl, isocyanato, thiocyanato, isothiocyanato, nitro, oxo,perhaloalkyl, perfluoroalkyl, phosphate, silyl, sulfinyl, sulfonyl,sulfonamidyl, sulfoxyl, sulfonate, urea, and amino, including mono- anddi-substituted amino groups, and the protected derivatives thereof.Di-substituted amino groups encompass those which form a ring togetherwith the nitrogen of the amino group, such as for instance, morpholino.The substituents themselves can be substituted, for example, acycloalkyl substituent can have a halide substituted at one or more ringcarbons, and the like. The protecting groups that can form theprotective derivatives of the above substituents are known to those ofskill in the art and can be found in references such as Greene and Wuts,above.

“Sulfanyl” refers to the groups: —S-(optionally substituted alkyl),—S-(optionally substituted aryl), —S-(optionally substitutedheteroaryl), and —S-(optionally substituted heterocycloalkyl).

“Sulfinyl” refers to the groups: —S(O)—H, —S(O)-(optionally substitutedalkyl), —S(O)-(optionally substituted amino), —S(O)-(optionallysubstituted aryl), —S(O)-(optionally substituted heteroaryl), and—S(O)-(optionally substituted heterocycloalkyl).

“Sulfonyl” refers to the groups: —S(O₂)—H, —S(O₂)-(optionallysubstituted alkyl), —S(O₂)-(optionally substituted amino),—S(O₂)-(optionally substituted aryl), —S(O₂)-(optionally substitutedhetero aryl), and —S(O₂)-(optionally substituted heterocycloalkyl).

“Sulfonamidyl” or “sulfonamido” refers to a —S(═O)₂—NRR or —N(R)—S(═O)₂—radical, where each R is selected independently from hydrogen, alkyl,cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) andheterocycloalkyl (bonded through a ring carbon). The R groups in —NRR ofthe —S(═O)₂—NRR radical can be taken together with the nitrogen to whichit is attached to form a 4-, 5-, 6-, or 7-membered ring. In someembodiments, it is a C₁-C₁₀ sulfonamido, wherein each R in sulfonamidocontains 1 carbon, 2 carbons, 3 carbons, or 4 carbons total. Asulfonamido group is optionally substituted by one or more of thesubstituents described for alkyl, cycloalkyl, aryl, and heteroarylrespectively.

“Sulfoxyl” refers to a —S(═O)₂OH radical.

“Sulfonate” refers to a —S(═O)₂—OR radical, where R is selected fromalkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) andheteroalicyclic (bonded through a ring carbon). A sulfonate group isoptionally substituted on R by one or more of the substituents describedfor alkyl, cycloalkyl, aryl, and heteroaryl respectively.

Where substituent groups are specified by their conventional chemicalformulae, written from left to right, they equally encompass thechemically identical substituents that would result from writing thestructure from right to left, e.g., —CH₂O— is equivalent to —OCH₂—.

In one aspect, provided herein is a compound of Formula I:

or pharmaceutically acceptable forms thereof, wherein,W_(a) ² is CR⁵ or N; W_(a) ³ is CR⁶ or N; W_(a) ⁴ is CR⁷ or N; whereinno more than two adjacent ring atoms selected from W_(a) ², W_(a) ³, andW_(a) ⁴ are heteroatoms;B is hydrogen, alkyl, amino, heteroalkyl, or a moiety of formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, andq is an integer of 0, 1, 2, 3, or 4;X is absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4;Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—,—N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is aninteger of 1, 2, 3, or 4;R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl,sulfonamido, halo, cyano, or nitro;each R² is independently alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate;R³ is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl,aralkyl, heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ isa heteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl, or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³;R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano, alkyl oramino;each R⁹ is independently hydrogen, alkyl, or heterocycloalkyl;

W_(d) is

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate;R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl, halo, —C(O)NH₂,aryl, heteroaryl, nonaromatic heterocyclyl, or cycloalkyl,R^(a′) is hydrogen, alkyl, —NH₂, cyano, or halogen; andeach R¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy, orhalogen.

In some embodiments, W_(a) ² is CR⁵ or N; W_(a) ³ is CR⁶ or N; W_(a) ⁴is CR⁷ or N wherein no more than two adjacent ring atoms selected fromW_(a) ², W_(a) ³, and W_(a) ⁴ are heteroatoms; B is hydrogen, alkyl,amino, heteroalkyl, or a moiety of the following formula:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, andq is an integer of 0, 1, 2, 3, or 4; X is absent or —(CH(R⁹))_(z)—, andz is an integer of 1, 2, 3, or 4; and Y is absent, —O—, —S—, —S(═O)—,—S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—, —N(R⁹)—, N(R⁹)—C(═O)—,—N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂, and z is an integer of 1, 2, 3, or 4.In some embodiments, R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy,amido, alkoxycarbonyl, sulfonamido, halo, cyano, or nitro; each R² isindependently alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl,aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy, amido, amino,acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy, nitro,phosphate, urea, or carbonate; and R³ is cycloalkyl, cycloalkylalkyl,aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl,heterocyclylalkyl, alkenyl, or alkynyl, or R³ is a heteroatom selectedfrom N, S, and O, wherein the heteroatom has a covalent bond eitherdirectly or through a C₁-C₆ alkyl group to an aryl, heteroaryl orheterocyclyl, or R³ and R⁵ are taken together with the carbons to whichthey are attached form a 5- or 6-membered ring; wherein each of theabove substituents can be substituted with 0, 1, 2, or 3 R¹³. In someembodiments, R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano,alkyl or amino; and each R⁹ is independently hydrogen, alkyl, orheterocycloalkyl;

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate; R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl,halo, —C(O)NH₂, aryl, heteroaryl, nonaromatic heterocyclyl, orcycloalkyl; R^(a′) is hydrogen, alkyl, —NH₂, cyano, or halogen; and eachR¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy, or halogen.

In another aspect, provided herein are compounds of Formula Ib:

or pharmaceutically acceptable forms thereof, whereinB is hydrogen, alkyl, amino, heteroalkyl, or a moiety of Formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl;q is an integer of 0, 1, 2, 3, or 4;X is absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4;Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—,—N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is aninteger of 1, 2, 3, or 4;R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl,sulfonamido, halo, cyano, or nitro;each R² is independently alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate;R³ is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl,aralkyl, heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ isa heteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl, or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³;R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano, alkyl oramino;each R⁹ is independently hydrogen, alkyl, or heterocycloalkyl;

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate;R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl, halo, —C(O)NH₂,aryl, heteroaryl, nonaromatic heterocyclyl, or cycloalkyl,R^(a′) is hydrogen, alkyl, —NH₂, cyano or halogen; andeach R¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy orhalogen.

In some embodiments of Formula II, W_(c) is aryl, heteroaryl,heterocycloalkyl, or cycloalkyl; q is an integer of 0, 1, 2, 3, or 4; Xis absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4; Y isabsent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—, —N(R⁹)—,N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is an integer of1, 2, 3, or 4. In some embodiments, R¹ is hydrogen, alkyl, alkenyl,alkynyl, alkoxy, amido, alkoxycarbonyl, sulfonamido, halo, cyano, ornitro; each R² is independently alkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate; R³ is cycloalkyl,cycloalkylalkyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl,heterocyclylalkyl, alkenyl, or alkynyl, or R³ is a heteroatom selectedfrom N, S, and O, wherein the heteroatom has a covalent bond eitherdirectly or through a C₁-C₆ alkyl group to an aryl, heteroaryl orheterocyclyl or R³ and R⁵ are taken together with the carbons to whichthey are attached form a 5- or 6-membered ring; wherein each of theabove substituents can be substituted with 0, 1, 2, or 3 R¹³; R⁵, R⁶,R⁷, and R⁸ are independently hydrogen, halo, cyano, alkyl or amino; andeach R⁹ is independently hydrogen, alkyl, or heterocycloalkyl.

In some embodiments, W_(d) is

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate; R¹² is H, alkyl, alkynyl, alkenyl, halo, aryl,heteroaryl, nonaromatic heterocyclyl, or cycloalkyl; R^(a′) is hydrogen,alkyl, —NH₂, cyano or halogen; and each R¹³ is independently hydrogen,C₁-C₆ alkyl, C₁-C₆ alkoxy or halogen.

In certain embodiments, R³ is selected from a 5-membered heteroaryl; a5-membered nonaromatic heterocycle; a 6-membered aryl; a 6-memberedheteroaryl; a 6-membered nonaromatic heterocycle; a fused 5/6-bicyclicheteroaryl; a fused 5/6-bicyclic nonaromatic heterocycle; a C₁-C₆ alkylgroup substituted with a 5-membered heteroaryl, a 5-membered nonaromaticheterocycle, a 6-membered aryl or heteroaryl, a 6-membered nonaromaticheterocycle, a fused 5/6-bicyclic heteroaryl, or a fused 5/6-bicyclicnonaromatic heterocycle. In some embodiments, R³ is a heteroatomselected from N, S, and O, wherein the heteroatom has a covalent bondeither directly or through a C₁-C₆ alkyl group to a 5-memberedheteroaryl, a 5-membered nonaromatic heterocycle, a 6-membered aryl orheteroaryl, a 6-membered nonaromatic heterocycle, a fused 5/6-bicyclicheteroaryl, or a fused 5/6-bicyclic nonaromatic heterocycle. In someembodiments, R³ is a C₁-C₆ alkyl group substituted with a fusedpolycyclic group, wherein the polycyclic group has greater than tworings and is carbocyclic or heterocyclic; C₁-C₆ alkyl group substitutedwith a bridged cycloalkyl or bridged heterocyclic group. In someembodiments, R³ is a C₁-C₆ alkyl group substituted with a spirocycliccycloalkyl or spirocyclic heterocyclic group. In some embodiments, R³ isa branched C₄-C₁₂ alkyl group, wherein said branched alkyl groupcontains at least one terminal t-butyl group. In compounds of FormulaI-B, W_(a) ² is CR⁵ or N; W_(a) ³ is CR⁶ or N; W_(a) ⁴ is CR⁷ or Nwherein no more than two adjacent ring atoms selected from W_(a) ²,W_(a) ³, and W_(a) ⁴ are heteroatoms; and B is hydrogen, alkyl, amino,heteroalkyl, cycloalkyl, heterocycloalkyl, or a moiety of Formula II:

In some embodiments of the compounds of Formula II, W_(c) is aryl,heteroaryl, heterocycloalkyl, or cycloalkyl, and q is an integer of 0,1, 2, 3, or 4. In some embodiments, X is absent or is —(CH(R⁹))_(z)—,and each instance of z is independently an integer of 1, 2, 3, or 4. Insome embodiments, Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂—, —N(R⁹)—,—C(═O)—(CHR⁹)_(z)—, —C(═O)—, —N(R⁹)—C(═O)—, or —N(R⁹)—C(═O)NH—,—N(R⁹)C(R⁹)₂—, or —C(═O)—(CHR⁹)_(z)—; wherein when W_(b) ⁵ is N, no morethan one of X or Y is absent. In some embodiments, R¹ is hydrogen,alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl,aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino,acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy, nitro,phosphate, urea, or carbonate. In some embodiments, each R² isindependently alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano,hydroxy, nitro, phosphate, urea, or carbonate. In some embodiments, R³is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl, aralkyl,heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ is aheteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³. In certain embodiments, R³ is selected from a 5-memberedheteroaryl; a 5-membered nonaromatic heterocycle; a 6-membered aryl; a6-membered heteroaryl; a 6-membered nonaromatic heterocycle; a fused5/6-bicyclic heteroaryl; a fused 5/6-bicyclic nonaromatic heterocycle; aC₁-C₆ alkyl group substituted with a 5-membered heteroaryl, a 5-memberednonaromatic heterocycle, a 6-membered aryl or heteroaryl, a 6-memberednonaromatic heterocycle, a fused 5/6-bicyclic heteroaryl, or a fused5/6-bicyclic nonaromatic heterocycle. In some embodiments, R³ is aheteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to a5-membered heteroaryl, a 5-membered nonaromatic heterocycle, a6-membered aryl or heteroaryl, a 6-membered nonaromatic heterocycle, afused 5/6-bicyclic heteroaryl, or a fused 5/6-bicyclic nonaromaticheterocycle. In some embodiments, R³ is a C₁-C₆ alkyl group substitutedwith a fused polycyclic group, wherein the polycyclic group has greaterthan two rings and is carbocyclic or heterocyclic; C₁-C₆ alkyl groupsubstituted with a bridged cycloalkyl or bridged heterocyclic group. Insome embodiments, R³ is a C₁-C₆ alkyl group substituted with aspirocyclic cycloalkyl or spirocyclic heterocyclic group. In someembodiments, R³ is a branched C₄-C₁₂ alkyl group, wherein said branchedalkyl group contains at least one terminal t-butyl group.

In another aspect, provided herein are compounds of Formula I-C:

or pharmaceutically acceptable forms thereof, whereinB is alkyl, amino, heteroalkyl, cycloalkyl, heterocycloalkyl, or amoiety of Formula II:

In some embodiments of Formula II, W_(c) is aryl, heteroaryl,heterocycloalkyl, or cycloalkyl, and q is an integer of 0, 1, 2, 3, or4; X is absent or —(CH(R⁹))_(z)—, and z is an integer of 1, 2, 3, or 4;Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂, —C(═O)—, —C(═O)(CHR⁹)_(z)—,—N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or —N(R⁹)C(R⁹)₂—, and z is aninteger of 1, 2, 3, or 4. In some embodiments, R¹ is hydrogen, alkyl,alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl, sulfonamido, halo,cyano, or nitro; each R² is independently alkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, arylalkyl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, halo, cyano, hydroxy, nitro, phosphate, urea, or carbonate;R³ is alkyl, alkenyl, or alkynyl; 5-membered heteroaryl; a 5-memberednonaromatic heterocycle; a 6-membered aryl; a 6-membered heteroaryl; a6-membered nonaromatic heterocycle; a fused 5/6-bicyclic heteroaryl; afused 5/6-bicyclic nonaromatic heterocycle; a C₁-C₆ alkyl groupsubstituted with a 5-membered heteroaryl, a 5-membered nonaromaticheterocycle, a 6-membered aryl or heteroaryl, a 6-membered nonaromaticheterocycle, a fused 5/6-bicyclic heteroaryl, or a fused 5/6-bicyclicnonaromatic heterocycle. In some embodiments, R³ is a heteroatomselected from N, S, and O, wherein the heteroatom has a covalent bondeither directly or through a C₁-C₆ alkyl group to a 5-memberedheteroaryl, a 5-membered nonaromatic heterocycle, a 6-membered aryl orheteroaryl, a 6-membered nonaromatic heterocycle, a fused 5/6-bicyclicheteroaryl, or a fused 5/6-bicyclic nonaromatic heterocycle. In someembodiments, R³ is a C₁-C₆ alkyl group substituted with a fusedpolycyclic group, wherein the polycyclic group has greater than tworings and is carbocyclic or heterocyclic; C₁-C₆ alkyl group substitutedwith a bridged cycloalkyl or bridged heterocyclic group. In someembodiments, R³ is a C₁-C₆ alkyl group substituted with a spirocycliccycloalkyl or spirocyclic heterocyclic group. In some embodiments, R³ isa branched C₄-C₁₂ alkyl group, wherein said branched alkyl groupcontains at least one terminal t-butyl group; R⁵, R⁶, R⁷, and R⁸ areindependently hydrogen, halo, cyano, alkyl or amino group; and each R⁹is independently hydrogen, alkyl, or heterocycloalkyl. In someembodiments, R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy,alkoxy, phosphate, urea, or carbonate; R¹² is H, alkyl, alkynyl,alkenyl, halo, aryl, heteroaryl, nonaromatic heterocyclyl, orcycloalkyl; R^(a′) is hydrogen, alkyl, —NH₂, cyano or halogen; and eachR¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy or halogen. Incertain embodiments, R³ and R⁵ taken together with the carbons to whichthey are attached can form a 5- or 6-membered ring. In some embodimentsof compounds of Formula I-C, R³ is C₂-C₁₀ alkyl, alkenyl or alkynyl,unsubstituted or substituted with alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, hydroxy, halo, cyano, trifluoromethyl,trifluoromethoxy, nitro, trimethylsilanyl, —OR^(a), —SR^(a),—OC(O)—R^(a), —N(R^(a))₂, —C(O)R^(a), —C(O)OR^(a), —OC(O)N(R^(a))₂,—C(O)N(R^(a))₂, —N(R^(a))C(O)OR^(a), —N(R^(a))C(O)R^(a),—N(R^(a))C(O)N(R^(a))₂, N(R^(a))C(NR^(a))N(R^(a))₂,—N(R^(a))S(O)_(t)R^(a) (where t is 1 or 2), —S(O)_(t)OR^(a) (where t is1 or 2), —S(O)_(t)N(R^(a))₂ (where t is 1 or 2), or PO₃(R^(a))₂ whereeach R^(a) is independently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl.

In some embodiments, the compound of Formula I is a compound having astructure of Formula IV:

or pharmaceutically acceptable forms thereof.

In some embodiments of the compound of Formula IV, R¹¹ is H, alkyl,halo, amino, amido, hydroxy, or alkoxy, and R¹² is H, alkyl, alkynyl,alkenyl, halo, aryl, heteroaryl, heterocycloalkyl, or cycloalkyl. Inanother embodiment, R¹¹ is amino and R¹² is alkyl, alkenyl, heteroaryl,aryl, or heterocycloalkyl. In some embodiments, R¹¹ is amino and R¹² iscyano, amino, carboxylic acid, alkoxycarbonyl, or amido.

The disclosure also provides compounds of Formula I having a structureof any of Formulae V, V-A, V-A1, V-A2, V-B, VI, VI-A, VII-A, VII-A1,VII-A2, VIII-A, VIII-A1, VIII-A2, IX-A, IX-A1, IX-A2, X-A, X-A1, X-A2,XI-A, XI-A1, XI-A2, XII-A, XII-A1, XII-A2, XIII-A, XIII-A1, XIII-A2,XIV-A, XIV-A1, XIV-A2, XV-A, XV-A1, XV-A2, XVI-A, XV1-A1, XVI-A2,XVII-A, XVII-A1, XVII-A2, XVIII-A, XVIII-A1, XVIII-A2, XIX-A, XIX-A2,XIX-A3, XX-A, XX-A2, XX-A3, XXI-A, XXI-A2, XXI-A3, XXII-A, XXII-A2 andXXII-A3:

Any of the disclosed elements and their substituents for the compoundsof Formula I can be used in any combination.

In some embodiments, B is unsubstituted or substituted alkyl, includingbut not limited to —(CH₂)₂—NR^(a)R^(a), wherein each R^(a) isindependently hydrogen, alkyl, fluoroalkyl, carbocyclyl,carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl,heterocycloalkylalkyl, heteroaryl or heteroarylalkyl, or NR^(a)R^(a) arecombined together to form a cyclic moiety, which includes but is notlimited to piperidinyl, piperazinyl, and morpholinyl. In someembodiments, B is unsubstituted or substituted amino. In someembodiments, B is unsubstituted or substituted heteroalkyl.

In some embodiments, B is a moiety of Formula II:

and wherein W_(c) is selected from unsubstituted or substituted aryl,substituted phenyl, unsubstituted or substituted heteroaryl including,but not limited to, pyridin-2-yl, pyridin-3-yl, pyridin-4-yl,pyrimidin-4-yl, pyrimidin-2-yl, pyrimidin-5-yl, or pyrazin-2-yl,unsubstituted or substituted monocyclic heteroaryl, unsubstituted orsubstituted bicyclic heteroaryl, a heteroaryl comprising two heteroatomsas ring atoms, unsubstituted or substituted heteroaryl comprising anitrogen ring atom, a heteroaryl comprising two nitrogen ring atoms, aheteroaryl comprising a nitrogen and a sulfur as ring atoms,unsubstituted or substituted heterocycloalkyl including, but not limitedto, morpholinyl, tetrahydropyranyl, piperazinyl, and piperidinyl, orunsubstituted or substituted cycloalkyl including, but not limited, andcyclopentyl and cyclohexyl.

In some embodiments, B is one of the following moieties:

In some embodiments, B is one of the following moieties:

In some embodiments, B is substituted by one or more of alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, halo, cyano, hydroxy or nitro, each of which alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkoxy, amido, amino, acyl, acyloxy, or sulfonamido, canitself be substituted.

In some embodiments, R¹ is selected from hydrogen, unsubstituted orsubstituted alkyl, unsubstituted or substituted heteroalkyl,unsubstituted or substituted alkenyl, unsubstituted or substitutedalkynyl, unsubstituted or substituted cycloalkyl, and unsubstituted orsubstituted heterocycloalkyl. In some embodiments, R¹ is unsubstitutedor substituted aryl, unsubstituted or substituted arylalkyl,unsubstituted or substituted heteroaryl, or unsubstituted or substitutedheteroarylalkyl. In some embodiments, R¹ is unsubstituted or substitutedalkoxy, unsubstituted or substituted amido, or unsubstituted orsubstituted amino. In some embodiments, R¹ is unsubstituted orsubstituted acyl, unsubstituted or substituted acyloxy, unsubstituted orsubstituted alkoxycarbonyl, or unsubstituted or substituted sulfonamido.In some embodiments, R¹ is halo which includes —Cl, —F, —I, and —Br. Insome embodiments, R¹ is selected from cyano, hydroxy, nitro,unsubstituted or substituted phosphate, unsubstituted or substitutedurea, and carbonate.

In some embodiments, when R¹ is alkyl, R¹ is methyl, ethyl, propyl,isopropyl, n-butyl, tert-butyl, sec-butyl, pentyl, hexyl or heptyl.

In some embodiments, when R¹ is alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, or hydroxy, R¹ is substituted by phosphate, unsubstitutedurea, substituted urea, carbonic acid, or carbonate.

In some embodiments, when R¹ is alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, orsulfonamido, R¹ is substituted by one or more of alkyl, heteroalkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl,heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy,alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy or nitro, each ofwhich alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl,heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy,amido, amino, acyl, acyloxy, alkoxycarbonyl, or sulfonamido can itselfbe substituted.

In some embodiments, q is an integer of 0. In some embodiments, q is aninteger of 1. In some embodiments, q is an integer of 2. In someembodiments, q is an integer of 3. In some embodiments, q is an integerof 4.

In some embodiments, R² is selected from unsubstituted or substitutedalkyl, unsubstituted or substituted heteroalkyl, unsubstituted orsubstituted alkenyl, unsubstituted or substituted alkynyl, unsubstitutedor substituted cycloalkyl, and unsubstituted or substitutedheterocycloalkyl. In some embodiments, R² is unsubstituted orsubstituted aryl, unsubstituted or substituted arylalkyl, unsubstitutedor substituted heteroaryl, or unsubstituted or substitutedheteroarylalkyl. In some embodiments, R² is unsubstituted or substitutedalkoxy, unsubstituted or substituted amido, or unsubstituted orsubstituted amino. In some embodiments, R² is unsubstituted orsubstituted acyl, unsubstituted or substituted acyloxy, unsubstituted orsubstituted alkoxycarbonyl, or unsubstituted or substituted sulfonamido.In some embodiments, R² is halo, which is —I, —F, —Cl, or —Br. In someembodiments, R² is selected from cyano, hydroxy, nitro, a carbonic acid,and a carbonate. In some embodiments, R² is unsubstituted or substitutedphosphate. In some embodiments, R² is unsubstituted or substituted urea.In some embodiments, when R² is alkyl, R² is methyl, ethyl, propyl,isopropyl, n-butyl, tert-butyl, sec-butyl, pentyl, hexyl or heptyl.

In some embodiments, when R² is alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, or hydroxy, it is substituted by phosphate, substituted byurea, or substituted by carbonate.

In some embodiments, when R² is alkyl, heteroalkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, orsulfonamido, R² is substituted by one or more of alkyl, heteroalkyl,alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl,alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo,cyano, hydroxy or nitro, each of which alkyl, heteroalkyl, alkenyl,alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, alkoxy, amido,amino, acyl, acyloxy, alkoxycarbonyl, or sulfonamido can itself besubstituted.

In some embodiments, R³ is a 5-membered heteroaryl group. Such groupsinclude, for example, pyrrole, furan, thiophene, triazole, oxazole,pyrazole, and isoxazole. In other embodiments, R³ is a 5-memberednonaromatic heterocycle, including, but not limited to, oxazoline andoxazolidinone. In still other embodiments, R³ is a 6-membered heteroarylgroup such as pyridine, pyrazine, pyrimidine and pyridazine. In anotherembodiment, R³ is a 6-membered nonaromatic heterocycle, includingmoieties such as morpholino or piperidino. In other embodiments, R³ is afused 5/6-bicyclic heteroaryl, for example benzothiazole, benzoxazole,benzisoxazole, indazole, benzimidazole, benzothiophene, indole,isoindole, purine, or pyrazolopyrimidine. In yet other embodiments, R³is a fused 5/6-bicyclic nonaromatic heterocycle.

In some embodiments, R³ is a C₁-C₆ alkyl group substituted with a5-membered heteroaryl, a 5-membered nonaromatic heterocycle, a6-membered heteroaryl, a 6-membered nonaromatic heterocycle, a fused5/6-bicyclic heteroaryl, or a fused 5/6-bicyclic nonaromaticheterocycle. In other embodiments, R³ is a heteroatom selected from N,S, and O, wherein the heteroatom has a covalent bond either directly orthrough a C₁-C₆ alkyl group to a 5-membered heteroaryl, a 5-memberednonaromatic heterocycle, a 6-membered heteroaryl, a 6-memberednonaromatic heterocycle, a fused 5/6-bicyclic heteroaryl, or a fused5/6-bicyclic nonaromatic heterocycle.

In other embodiments, R³ is a C₁-C₆ alkyl group substituted with a fusedpolycyclic group, wherein the polycyclic group has greater than tworings and is carbocyclic or heterocyclic; C₁-C₆ alkyl group substitutedwith a bridged cycloalkyl or bridged heterocyclic group; C₁-C₆ alkylgroup substituted with a spirocyclic cycloalkyl or spirocyclicheterocyclic group; or branched C₄-C₁₂ alkyl group, wherein saidbranched alkyl group contains at least one terminal t-butyl group.

Each of the embodiments named above for R³ is unsubstituted oroptionally additionally substituted with an alkyl, heteroalkyl, alkenyl,alkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, alkoxy, amido,amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxyor nitro group.

In certain embodiments, R³ is a substituted or unsubstituted groupselected from pyridine, pyrazole, piperazine, and pyrrolidine, whereinthe substituent can be a C₁-C₆ alkyl group or a halogen.

In some embodiments, a compound is provided wherein R³ is selected froma 5-membered heteroaryl selected from pyrrole, a furan, and a thiophenegroup; 5-membered nonaromatic heterocycle selected from a pyrrolidine, atetrahydrofuran, and a tetrahydrothiophene group; 6-membered heteroarylselected from pyridine, pyrazine, pyrimidine, and pyridazine; 6-memberednonaromatic heterocycle selected from piperidine, tetrahydropyran, andthiane; and fused 5/6-bicyclic heteroaryl selected from indole,isoindole, benzofuran, isobenzofuran, benzothiophene, benzimidazole,indazole, benzoxazole, benzisoxazole, and purine. In certainembodiments, R³ is a substituted or unsubstituted group selected frompyridine, pyrazole, piperazine, and pyrrolidine. By way of non-limitingexample, the R³ group can be substituted with a C₁-C₆ alkyl group or ahalogen. For example, the R³ group can be substituted with a methylgroup.

In some embodiments, a compound is provided wherein R³ is selected from

wherein R¹³ is H or C₁-C₆ alkyl. In certain embodiments, R¹³ is methyl.In some embodiments, R³ is selected from the following:

In some embodiments, R⁵, R⁶, R⁷, and R⁸ are each independently hydrogen,unsubstituted or substituted alkyl (including, but not limited to,unsubstituted or substituted C₁-C₄ alkyl). In some embodiments, R⁵, R⁶,R⁷, and R⁸ are each independently unsubstituted or substituted alkenylincluding, but not limited to, unsubstituted or substituted C₂-C₅alkenyl. In some embodiments, R⁵, R⁶, R⁷, and R⁸ are each independentlyunsubstituted or substituted alkynyl including, but not limited to,unsubstituted or substituted C₂-C₅ alkynyl. In some embodiments, R⁵, R⁶,R⁷, and R⁸ are each independently unsubstituted or substitutedcycloalkyl including, but not limited to, unsubstituted or substitutedC₃-C₅ cycloalkyl. In some embodiments, R⁵, R⁶, R⁷, and R⁸ are eachindependently unsubstituted or substituted heterocycloalkyl. In someembodiments, R⁵, R⁶, R⁷, and R⁸ are each independently unsubstituted orsubstituted heteroalkyl including, but not limited to, unsubstituted orsubstituted C₁-C₄ heteroalkyl. In some embodiments, R⁵, R⁶, R⁷, and R⁸are each independently unsubstituted or substituted alkoxy including,but not limited to, unsubstituted or substituted C₁-C₄ alkoxy. In someembodiments, R⁵, R⁶, R⁷, and R⁸ are each independently unsubstituted orsubstituted amido including, but not limited to, unsubstituted orsubstituted C₁-C₄ amido. In some embodiments, R⁵, R⁶, R⁷, and R⁸ areeach independently unsubstituted or substituted amino. In someembodiments, R⁵, R⁶, R⁷, and R⁸ are each independently unsubstituted orsubstituted acyl, unsubstituted or substituted acyloxy, unsubstituted orsubstituted C₁-C₄ acyloxy, unsubstituted or substituted alkoxycarbonyl,unsubstituted or substituted sulfonamido, or unsubstituted orsubstituted C₁-C₄ sulfonamido. In some embodiments, R⁵, R⁶, R⁷, and R⁸are each independently halo, which is —I, —F, —Cl, or —Br. In someembodiments, R⁵, R⁶, R⁷, and R⁸ are each independently selected fromcyano, hydroxy, and nitro. In some other embodiments, R⁵, R⁶, R⁷, and R⁸are each independently —CH₃, —CH₂CH₃, n-propyl, isopropyl, —OCH₃,—OCH₂CH₃, or —CF₃.

In some embodiments, when R⁵, R⁶, R⁷, and R⁸ are each independentlyalkyl, alkenyl, alkynyl, cycloalkyl, heteroalkyl, acyl, alkoxy, amido,amino, acyloxy, alkoxycarbonyl, or sulfonamido, R⁵, R⁶, R⁷, and R⁸ areeach independently optionally substituted with one or more of alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, halo, cyano, hydroxy or nitro, each of which alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, orsulfonamido can itself be substituted.

In some embodiments, R⁵, R⁶, R⁷, and R⁸ are H.

In some embodiments, X is absent. In some embodiments, X is—(CH(R⁹))_(z), and z is an integer of 1, 2, 3 or 4.

In some embodiments, R⁹ is unsubstituted or substituted alkyl including,but not limited to, unsubstituted or substituted C₁-C₁₀ alkyl. In someembodiments, R⁹ is unsubstituted or substituted cycloalkyl including butnot limited to unsubstituted or substituted C₃-C₇ cycloalkyl. In someembodiments, R⁹ is ethyl, methyl or hydrogen. In some embodiments, R⁹ isunsubstituted or substituted heterocycloalkyl including, but not limitedto, unsubstituted or substituted C₂-C₁₀ heteroalkyl. In someembodiments, R⁹ is unsubstituted or substituted heteroalkyl including,but not limited to, unsubstituted or substituted C₂-C₁₀heteroalkyl.

In some embodiments, provided herein is a compound of Formula I (e.g., acompound of formula (I), (Ia), (Ib) or (Ic)) wherein R⁹ is hydrogen, andX is —CH₂—, —CH₂CH₂—, —CH₂CH₂CH₂—, —CH(CH₃)—, or —CH(CH₂CH₃)—. In otherembodiments, X is —(CH(R⁹))_(z), R⁹ is alkyl, or heterocycloalkyl, and zis an integer of 1. When X is —CH(R⁹)— and R⁹ is alkyl, orheterocycloalkyl, then the compound can adopt either an (S)- or(R)-stereochemical configuration with respect to carbon X. In someembodiments, the compound is a racemic mixture of (S)- and (R)-isomerswith respect to carbon X. In other embodiments, provided herein is amixture of compounds of Formula I wherein individual compounds of themixture exist predominately in an (S)- or (R)-isomeric configuration.For example, the compound mixture has an (S)-enantiomeric excess ofgreater than about 55%, about 60%, about 65%, about 70%, about 75%,about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about98%, about 99%, about 99.5%, or more at the X carbon. In otherembodiments, the compound mixture has an (S)-enantiomeric excess ofgreater than about 55% to about 99.5%, greater than about 60% to about99.5%, greater than about 65% to about 99.5%, greater than about 70% toabout 99.5%, greater than about 75% to about 99.5%, greater than about80% to about 99.5%, greater than about 85% to about 99.5%, greater thanabout 90% to about 99.5%, greater than about 95% to about 99.5%, greaterthan about 96% to about 99.5%, greater than about 97% to about 99.5%,greater than about 98% to greater than about 99.5%, greater than about99% to about 99.5%, or more.

In other embodiments, the compound mixture has an (R)-enantiomericpurity of greater than about 55%, about 60%, about 65%, about 70%, about75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%,about 98%, about 99%, about 99.5% or more at the X carbon. In some otherembodiments, the compound mixture has an (R)-enantiomeric excess ofgreater than about 55% to about 99.5%, greater than about 60% to about99.5%, greater than about 65% to about 99.5%, greater than about 70% toabout 99.5%, greater than about 75% to about 99.5%, greater than about80% to about 99.5%, greater than about 85% to about 99.5%, greater thanabout 90% to about 99.5%, greater than about 95% to about 99.5%, greaterthan about 96% to about 99.5%, greater than about 97% to about 99.5%,greater than about 98% to greater than about 99.5%, greater than about99% to about 99.5% or more.

In other embodiments, the compound mixture contains identical chemicalentities except for their stereochemical orientations, namely (S)- or(R)-isomers. For instance, in the compounds of Formula I, when X is—CH(R⁹)—, and R⁹ is not hydrogen, then the —CH(R⁹)— is in an (S)- or(R)-stereochemical orientation for each of the identical chemicalentities. In some embodiments, the mixture of identical chemicalentities of Formula I is a racemic mixture of (S)- and (R)-isomers atthe carbon represented by X. In another embodiment, the mixture of theidentical chemical entities (except for their stereochemicalorientations), contain predominately (S)-isomers or predominately(R)-isomers. For example, the (S)-isomers in the mixture of identicalchemical entities are present at about 55%, about 60%, about 65%, about70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%,about 97%, about 98%, about 99%, about 99.5%, or more, relative to the(R)-isomers. In some embodiments, the (S)-isomers in the mixture ofidentical chemical entities are present at an (S)-enantiomeric excess ofgreater than about 55% to about 99.5%, greater than about 60% to about99.5%, greater than about 65% to about 99.5%, greater than about 70% toabout 99.5%, greater than about 75% to about 99.5%, greater than about80% to about 99.5%, greater than about 85% to about 99.5%, greater thanabout 90% to about 99.5%, greater than about 95% to about 99.5%, greaterthan about 96% to about 99.5%, greater than about 97% to about 99.5%,greater than about 98% to greater than about 99.5%, greater than about99% to about 99.5% or more.

In another embodiment, the (R)-isomers in the mixture of identicalchemical entities (except for their stereochemical orientations), arepresent at about 55%, about 60%, about 65%, about 70%, about 75%, about80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%,about 99%, about 99.5%, or more, relative to the (S)-isomers. In someembodiments, the (R)-isomers in the mixture of identical chemicalentities (except for their stereochemical orientations), are present ata (R)-enantiomeric excess greater than about 55% to about 99.5%, greaterthan about 60% to about 99.5%, greater than about 65% to about 99.5%,greater than about 70% to about 99.5%, greater than about 75% to about99.5%, greater than about 80% to about 99.5%, greater than about 85% toabout 99.5%, greater than about 90% to about 99.5%, greater than about95% to about 99.5%, greater than about 96% to about 99.5%, greater thanabout 97% to about 99.5%, greater than about 98% to greater than about99.5%, greater than about 99% to about 99.5%, or more.

In some embodiments, the compound of Formula I, X is —CH(R⁹)—, R⁹ ismethyl or ethyl, and the compound is the (S)-isomer.

In some embodiments of the compound of Formula I, Y is absent. In someembodiments, Y is —O—, —S—, —S(═O)—, —S(═O)₂—, —C(═O)—, —N(R⁹)(C═O)—,—N(R⁹)(C═O)NH—, —N(R⁹)C(R⁹)₂— (such as —N(R⁹)CH₂—, specifically—N(CH₃)CH₂—, N(CH(CH₃)₂)CH₂— or N(CH₂CH₃)CH₂—), —N(R⁹)—, —N(CH₃)—,—N(CH₂CH₃)—, or —N(CH(CH₃)₂)—. In some embodiments, Y is—C(═O)—(CHR⁹)_(z)— and z is an integer of 1, 2, 3, or 4.

In some embodiments, at least one of X and Y is present. In someembodiments of the compound of Formula I, —XY— is —CH₂—, —CH₂—N(CH₃),—CH₂—N(CH₂CH₃), —CH(CH₃)—NH—, (S)-CH(CH₃)—NH—, or (R)-CH(CH₃)—NH—. Inother embodiments, X—Y is —N(CH₃)—CH₂—, N(CH₂CH₃)CH₂—, —N(CH(CH₃)₂)CH₂—,or —NHCH₂—. In some embodiments, other compounds of Formula I areprovided wherein when X—Y is X is —(CH(R⁹))_(z)N(R⁹)—, z is an integerof 1, 2, 3 or 4, and —N(R⁹)— is not —NH—, then —XY— is not connected topurinyl.

In some embodiments, W_(d) in a formula disclosed herein (including butnot limited to I, I-1, IV, IV-A, V, V-A, V-A2, V-B, VI and VI-A), isselected from unsubstituted or substituted heterocycloalkyl,unsubstituted or substituted aryl, and unsubstituted or substitutedheteroaryl.

In various embodiments, W_(d) is unsubstituted or substituted monocyclicheteroaryl (including, but not limited to, pyrimidinyl, pyrrolyl,pyrazinyl, triazinyl, or pyridazinyl) or unsubstituted or substitutedbicyclic heteroaryl.

In some embodiments, W_(d) is a monocyclic heteroaryl of the followingformula:

wherein R^(a′) is hydrogen, halo, phosphate, urea, a carbonate,unsubstituted or substituted amino, unsubstituted or substituted alkyl,unsubstituted or substituted alkenyl, unsubstituted or substitutedalkynyl, unsubstituted or substituted cycloalkyl, unsubstituted orsubstituted heteroalkyl, or unsubstituted or substitutedheterocycloalkyl; and R¹² is hydrogen, unsubstituted or substitutedalkyl, unsubstituted or substituted cyano, unsubstituted or substitutedalkynyl, unsubstituted or substituted alkenyl, halo, unsubstituted orsubstituted aryl, unsubstituted or substituted heteroaryl, unsubstitutedor substituted heterocycloalkyl, unsubstituted or substitutedcycloalkyl, unsubstituted or substituted amino, carboxylic acid,unsubstituted or substituted alkoxycarbonyl, unsubstituted orsubstituted amido, unsubstituted or substituted acyl, or unsubstitutedor substituted sulfonamido.

Provided herein are monocyclic heteroaryl W_(d) including, but notlimited to, one of the following formulae:

In some embodiments, W_(d) in a formula disclosed herein (including butnot limited to I, I-1, IV, IV-A, V, V-A, V-A2, V-B, VI and VI-A), is abicyclic heteroaryl having at least one heteroatom, e.g., a bicyclicheteroaryl having at least one nitrogen ring atom. In some embodiments,W_(d) is a bicyclic heteroaryl having at least two heteroatoms, e.g., abicyclic heteroaryl having at least two nitrogen ring atoms. In someembodiments, W_(d) is a bicyclic heteroaryl having two heteroatoms inthe ring which is connected to XY. In some embodiments, W_(d) is abicyclic heteroaryl having two nitrogen ring atoms in the ring to whichXY is connected. In some embodiments, W_(d) is a bicyclic heteroarylhaving four heteroatoms, e.g, a bicyclic heteroaryl having four nitrogenring atoms. In some embodiments, W_(d) is unsubstituted or substituted4-amino-1H-pyrazolo[3,4-d]pyrimidin-1-yl, unsubstituted or substituted7-amino-2-methyl-2H-pyrazolo[4,3-d]pyrimidin-3-yl, unsubstituted orsubstituted 6-methylenyl-9H-purin-6-yl, or unsubstituted or substituted6-amino-9H-purin-9-yl.

In some embodiments W_(d) is one of the following:

wherein R^(a′) is hydrogen, halo, phosphate, urea, a carbonate,unsubstituted or substituted amino, unsubstituted or substituted alkyl,unsubstituted or substituted alkenyl, unsubstituted or substitutedalkynyl, unsubstituted or substituted cycloalkyl, unsubstituted orsubstituted heteroalkyl, or unsubstituted or substitutedheterocycloalkyl; R¹¹ is hydrogen, unsubstituted or substituted alkyl,halo (which includes —I, —F, —Cl, or —Br), unsubstituted or substitutedamino, unsubstituted or substituted amido, hydroxy, or unsubstituted orsubstituted alkoxy, phosphate, unsubstituted or substituted urea, orcarbonate; and R¹² is H, unsubstituted or substituted alkyl,unsubstituted or substituted cyano, unsubstituted or substitutedalkynyl, unsubstituted or substituted alkenyl, halo, unsubstituted orsubstituted aryl, unsubstituted or substituted heteroaryl, unsubstitutedor substituted heterocycloalkyl, unsubstituted or substitutedcycloalkyl, unsubstituted or substituted amino, carboxylic acid,unsubstituted or substituted alkoxycarbonyl, unsubstituted orsubstituted amido, unsubstituted or substituted acyl, or unsubstitutedor substituted sulfonamido.

In certain embodiments, W_(d) is

wherein R^(a′) and R¹² are as defined herein.

In some embodiments of W_(d) of the compounds of Formula I, when R^(a′)is alkyl, alkynyl, cycloalkyl, heteroalkyl, or heterocycloalkyl, it issubstituted by phosphate, urea, or carbonate.

In some embodiments of W_(d) of the compounds of Formula I, when R¹¹ isalkyl, amino, amido, hydroxy, or alkoxy, it is substituted by phosphate,urea, or carbonate.

In some embodiments of the compound of Formula I, —X—Y—W_(d) is one ofthe following moieties:

In some embodiments of the compound of Formula I, R¹² is selected fromhydrogen, cyano, halo, unsubstituted or substituted alkyl, unsubstitutedor substituted alkynyl, and unsubstituted or substituted alkenyl. Insome embodiments, R¹² is unsubstituted or substituted aryl. In someembodiments, R¹² is unsubstituted or substituted heteroaryl, whichincludes, but is not limited to, heteroaryl having a five membered ring,heteroaryl having a six membered ring, heteroaryl with at least onenitrogen ring atom, heteroaryl with two nitrogen ring atoms, monocylicheteroaryl, and bicylic heteroaryl. In some embodiments, R¹² isunsubstituted or substituted heterocycloalkyl, which includes, but isnot limited to, heterocycloalkyl with one nitrogen ring atom,heterocycloalkyl with one oxygen ring atom, heterocycloalkyl with onesulfur ring atom, 5 membered heterocycloalkyl, 6 memberedheterocycloalkyl, saturated heterocycloalkyl, unsaturatedheterocycloalkyl, heterocycloalkyl having an unsaturated moietyconnected to the heterocycloalkyl ring, heterocycloalkyl substituted byoxo, and heterocycloalkyl substituted by two oxo. In some embodiments,R¹² is unsubstituted or substituted cycloalkyl, including but notlimited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloalkylsubstituted by one oxo, or cycloalkyl having an unsaturated moietyconnected to the cycloalkyl ring. In some embodiments, R¹² isunsubstituted or substituted amido, carboxylic acid, unsubstituted orsubstituted acyloxy, unsubstituted or substituted alkoxycarbonyl,unsubstituted or substituted acyl, or unsubstituted or substitutedsulfonamido.

In some embodiments, when R¹² is alkyl, alkynyl, alkenyl, aryl,heteroaryl, heterocycloalkyl, or cycloalkyl, it is substituted withphosphate. In some embodiments, when R¹² is alkyl, alkynyl, alkenyl,aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, it is substitutedwith urea. In some embodiments, when R¹² is alkyl, alkynyl, alkenyl,aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, it is substitutedwith carbonate.

In some embodiments, when R¹² is alkyl, alkynyl, alkenyl, aryl,heteroaryl, heterocycloalkyl, cycloalkyl, alkoxycarbonyl, amido,acyloxy, acyl, or sulfonamido, it is substituted with one or more ofalkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl,aryl, heteroaryl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, halo, cyano, hydroxy or nitro, each of which alkyl,heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl,heteroaryl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, orsulfonamido can itself be substituted.

In some embodiments, R¹² of W_(d) is one of the following moieties:

In some embodiments, W_(d) is a pyrazolopyrimidine of Formula III:

wherein R¹¹ is H, alkyl, halo, amino, amido, hydroxy, or alkoxy, and R¹²is H, alkyl, alkynyl, alkenyl, halo, aryl, heteroaryl, heterocycloalkyl,or cycloalkyl. In some embodiments, R¹¹ is amino and R¹² is H, alkyl,alkynyl, alkenyl, halo, aryl, heteroaryl, heterocycloalkyl, orcycloalkyl. In some embodiments, R¹¹ is amino and R¹² is alkyl, halo,aryl, heteroaryl, heterocycloalkyl, or cycloalkyl. In some embodiments,R¹¹ is amino and R¹² is monocyclic heteroaryl. In some embodiments, R¹¹is amino and R¹² is bicyclic heteroaryl. In some embodiments, R¹¹ isamino and R¹² is cyano, amino, carboxylic acid, acyloxy, alkoxycarbonyl,or amido.

In some embodiments, the compound of Formula I is a compound which has astructure selected from Formula XXIII-A, XXIII-B, XXIV-A, XXIV-B, XXV,XXVI, XXVI-A, XXVII, XXVII-A, XXVII-B, XXVII-C, XXVII-C1, XXVII-C2,XXVII-D, and XXVII-D:

In another embodiment, the compound of Formula I is a compound which hasa structure selected from Formula XXVIII, XXVIII-A, XXIX, XXIX-A, andXXIX-A1:

In one aspect, for compounds described herein, R₃ is H, CH₃, CF₃, Cl, F,aryl, or heteroaryl; B is alkyl or a moiety of Formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl; R¹is H, —F, —Cl, —CN, —CH₃, isopropyl, —CF₃, —OCH₃, nitro, or phosphate;R² is halo, hydroxy, cyano, nitro, or phosphate; q is an integer of 0,1, 2, 3, or 4; R⁵, R⁶, R⁷, and R⁸ are H; X is absent or (CH₂)_(z); z is1; Y is absent, —N(R⁹)—, or —N(R⁹)CH(R⁹)—; R⁹ is hydrogen, C₁-C₁₀ alkyl,C₃-C₇ cycloalkyl, or C₂-C₁₀ heteroalkyl; and W_(d) is pyrazolopyrimidineor purine.

TABLE 1 Illustrative B moieties of compounds of Formula I include, butare not limited to: Sub-class # B B-1

B-2

B-3 —CH(CH₃)₂ B-4

B-5

B-6

B-7

B-8

B-9

B-10

B-11

B-12

B-13

B-14

B-15

B-16

B-17

B-18

B-19

B-20

B-21

B-22

B-23

B-24

B-25

B-26

B-27

B-28

B-29

B-30

B-31

B-32

B-33

B-34

B-35

B-36

B-37

B-38

B-39

B-40

B-41

B-42

B-43

B-44

B-45

B-46

B-47

B-48

B-49

B-50

B-51

B-52

B-53

B-54

B-55

B-56

B-57

B-58

B-59

B-60

B-61

B-62

B-63

B-64

B-65

B-66

B-67

B-68

B-69

B-70

B-71

B-72

B-73

B-74

B-75

B-76

B-77

B-78

B-79

B-80

B-81

B-82

B-83

B-84

B-85

B-86

B-87 —CH₃ B-88 —CH₂CH₃ B-89

B-90

B-91

B-92

B-93

B-94

B-95

B-96

B-97

B-98

B-99

B-100

B-101

B-102

TABLE 2 Illustrative R¹² moieties of compounds of Formula I include, butare not limited to: Sub-class R¹² 12-1 —CN 12-2 —Br 12-3 —Cl 12-4—CH₂CH₃ 12-5 —CH₃ 12-6 —CH(CH₃)₂ 12-7

12-8

12-9

12-10

12-11

12-12

12-13

12-14

12-15

12-16

12-17

12-18

12-19

12-20

12-21

12-22

12-23

12-24

12-25

12-26

12-27

12-28

12-29

12-30

12-31

12-32

12-33

12-34

12-35 —H 12-36

12-37

12-38

12-39

12-40

12-41

12-42

12-43

12-44

12-45

12-46

12-47

12-48

12-49

12-50

12-51

12-52

12-53

12-54

12-55

12-56

12-57

12-58

12-59

12-60

12-61 —I 12-62

12-63

12-64

12-65

12-66

12-67

12-68

12-69

12-70

12-71

12-72

12-73

12-74

12-75

12-76

12-77

12-78

12-79

12-80

12-81

12-82

12-83

12-84

12-85

12-86

12-87

12-88

12-89

12-90

12-91

12-92

12-93

12-94

12-95

12-96

TABLE 3 Illustrative X—Y—W_(d) of compounds of Formula I include, butare not limited to: Sub-class X—Y—W_(d) 1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

In some embodiments, one or more subject compounds bind specifically toa PI3 kinase.

In some embodiments, the IC₅₀ of a subject compound for p110α, p110β,p110γ, or p110δ is less than about 1 uM, less than about 100 nM, lessthan about 50 nM, less than about 10 nM, less than 1 nM or even lessthan about 0.5 nM. In some embodiments, the IC₅₀ of a subject compoundfor mTor is less than about 1 μM, less than about 100 nM, less thanabout 50 nM, less than about 10 nM, less than 1 nM or even less thanabout 0.5 nM. In some other embodiments, one or more subject compoundsexhibit dual binding specificity and are capable of inhibiting a PI3kinase (e.g., a class I PI3 kinase) as well as a protein kinase (e.g.,mTor) with an IC₅₀ value less than about 1 μM, less than about 100 nM,less than about 50 nM, less than about 10 nM, less than 1 nM or evenless than about 0.5 nM. One or more subject compounds are capable ofinhibiting tyrosine kinases including, for example, DNA-dependentprotein kinase DNA-dependent protein kinase (Pubmed protein accessionnumber (PPAN) AAA79184), Abl tyrosine kinase (CAA52387), Bcr-Abl,hemopoietic cell kinase (PPAN CAI19695), Src (PPAN CAA24495), vascularendothelial growth factor receptor 2 (PPAN ABB82619), vascularendothelial growth factor receptor-2 (PPAN ABB82619), epidermal growthfactor receptor (PPAN AG43241), EPH receptor B4 (PPAN EAL23820), stemcell factor receptor (PPAN AAF22141), Tyrosine-protein kinase receptorTIE-2 (PPAN Q02858), fms-related tyrosine kinase 3 (PPAN NP_(—)004110),platelet-derived growth factor receptor alpha (PPAN NP_(—)990080), RET(PPAN CAA73131), and functional mutants thereof. In some embodiments,the tyrosine kinase is Abl, Bcr-Abl, EGFR, or Flt-3, and any otherkinases listed in the Tables herein.

In some embodiments, non-limiting exemplary compounds exhibit one ormore functional characteristics disclosed herein. For example, one ormore subject compounds bind specifically to a PI3 kinase. In someembodiments, the IC₅₀ of a subject compound for p110α, p110β, p110γ, orp110δ is less than about 1 μM, less than about 100 nM, less than about50 nM, less than about 10 nM, less than about 1 nM, less than about 0.5nM, less than about 100 pM, or less than about 50 pM.

In some embodiments, one or more of the subject compound can selectivelyinhibit one or more members of type I or class I phosphatidylinositol3-kinases (PI3-kinase) with an IC₅₀ value of about 100 nM, 50 nM, 10 nM,5 nM, 100 pM, 10 pM or 1 pM, or less as measured in an in vitro kinaseassay.

In some embodiments, one or more of the subject compounds canselectively inhibit one or two members of type I or class Iphosphatidylinositol 3-kinases (PI3-kinase) such as PI3-kinase α,PI3-kinase β, PI3-kinase γ, and PI3-kinase δ. In some aspects, some ofthe subject compounds selectively inhibit PI3-kinase δ as compared toall other type I PI3-kinases. In other aspects, some of the subjectcompounds selectively inhibit PI3-kinase δ and PI3-kinase γ as comparedto the rest of the type I PI3-kinases. In yet other aspects, some of thesubject compounds selectively inhibit PI3-kinase α and PI3-kinase β ascompared to the rest of the type I PI3-kinases. In still yet some otheraspects, some of the subject compounds selectively inhibit PI3-kinase δand PI3-kinase α as compared to the rest of the type I PI3-kinases. Instill yet some other aspects, some of the subject compounds selectivelyinhibit PI3-kinase δ and PI3-kinase β as compared to the rest of thetype I PI3-kinases, or selectively inhibit PI3-kinase δ and PI3-kinase αas compared to the rest of the type I PI3-kinases, or selectivelyinhibit PI3-kinase α and PI3-kinase γ as compared to the rest of thetype I PI3-kinases, or selectively inhibit PI3-kinase γ and PI3-kinase βas compared to the rest of the type I PI3-kinases.

In yet another aspect, an inhibitor that selectively inhibits one ormore members of type I PI3-kinases, or an inhibitor that selectivelyinhibits one or more type I PI3-kinase mediated signaling pathways,alternatively can be understood to refer to a compound that exhibits a50% inhibitory concentration (IC₅₀) with respect to a given type IPI3-kinase, that is at least about 10-fold, at least about 20-fold, atleast about 50-fold, at least about 100-fold, at least about 1000-fold,at least about 10,000-fold, or lower, than the inhibitor's IC₅₀ withrespect to the rest of the other type I PI3-kinases. In one embodiment,an inhibitor selectively inhibits PI3-kinase δ as compared to PI3-kinaseβ with at least about 10-fold lower IC₅₀ for PI3-kinase δ. In certainembodiments, the IC₅₀ for PI3-kinase δ is below about 100 nM, while theIC₅₀ for PI3-kinase β is above about 1000 nM. In certain embodiments,the IC₅₀ for PI3-kinase δ is below about 50 nM, while the IC₅₀ forPI3-kinase β is above about 5000 nM. In certain embodiments, the IC₅₀for PI3-kinase δ is below about 10 nM, while the IC₅₀ for PI3-kinase βis above about 1000 nM, above about 5,000 nM, or above about 10,000 nM.

Pharmaceutical Compositions

In some embodiments, provided herein are pharmaceutical compositionscomprising one or more compounds as disclosed herein and one or morepharmaceutically acceptable excipients. In some embodiments, thepharmaceutical composition comprises a compound as disclosed herein andone or more pharmaceutically acceptable excipients.

In some embodiments, provided herein are pharmaceutical compositions fortreating diseases or conditions related to an undesirable, over-active,harmful or deleterious immune response in a subject. Such undesirableimmune response can be associated with or result in, e.g., asthma,emphysema, bronchitis, psoriasis, allergy, anaphylaxsis, auto-immunediseases, rhuematoid arthritis, graft versus host disease, and lupuserythematosus. The pharmaceutical compositions can be used to treatother respiratory diseases including, but not limited to, diseasesaffecting the lobes of the lung, pleural cavity, bronchial tubes,trachea, upper respiratory tract, or the nerves and muscle responsiblefor breathing.

In some embodiments, provided herein are pharmaceutical compositions forthe treatment of multiorgan failure. Also provided herein arepharmaceutical compositions for the treatment of liver diseases(including diabetes), gall bladder disease (including gallstones),pancreatitis or kidney disease (including proliferativeglomerulonephritis and diabetes-induced renal disease) or pain in asubject.

In some embodiments, provided herein are pharmaceutical compositions forthe prevention of blastocyte implantation in a subject.

In some embodiments, provided herein are pharmaceutical compositions fortreating a disease related to vasculogenesis or angiogenesis in asubject which can manifest as tumor angiogenesis, chronic inflammatorydisease such as rheumatoid arthritis, inflammatory bowel disease,atherosclerosis, skin diseases such as bullous pemphigoid (BP),psoriasis, eczema, and scleroderma, diabetes, diabetic retinopathy,retinopathy of prematurity, age-related macular degeneration,hemangioma, glioma, melanoma, Kaposi's sarcoma and ovarian, breast,lung, pancreatic, prostate, colon and epidermoid cancer.

In some embodiments, provided herein are pharmaceutical compositions forthe treatment of disorders involving platelet aggregation or plateletadhesion, including but not limited to Idiopathic thrombocytopenicpurpura, Bernard-Soulier syndrome, Glanzmann's thrombasthenia, Scott'ssyndrome, von Willebrand disease, Hermansky-Pudlak Syndrome, and Grayplatelet syndrome.

In some embodiments, pharmaceutical compositions are provided fortreating a disease which is skeletal muscle atrophy, skeletal or musclehypertrophy. In some embodiments, provided herein are pharmaceuticalcompositions for the treatment of disorders that include, but are notlimited to, cancers as discussed herein, transplantation-relateddisorders (e.g., lowering rejection rates, graft-versus-host disease,etc.), muscular sclerosis (MS), allergic disorders (e.g., arthritis,allergic encephalomyelitis) and other immunosuppressive-relateddisorders, metabolic disorders (e.g., diabetes), reducing intimalthickening following vascular injury, and misfolded protein disorders(e.g., Alzheimer's Disease, Gaucher's Disease, Parkinson's Disease,Huntington's Disease, cystic fibrosis, macular degeneration, retinitispigmentosa, and prion disorders) (as mTOR inhibition can alleviate theeffects of misfolded protein aggregates). The disorders also includehamartoma syndromes, such as tuberous sclerosis and Cowden Disease (alsotermed Cowden syndrome and multiple hamartoma syndrome)

In some embodiments, the disclosure provides a pharmaceuticalcomposition for treating ophthalmic disorders. The pharmaceuticalcomposition is formulated for ocular administration and it contains aneffective amount of a compound as disclosed herein and a pharmaceuticalexcipient suitable for ocular administration. Pharmaceuticalcompositions suitable for ocular administration can be presented asdiscrete dosage forms, such as drops or sprays each containing apredetermined amount of an active ingredient a solution, or a suspensionin an aqueous or non-aqueous liquid, an oil-in-water emulsion, or awater-in-oil liquid emulsion. Eye drops can be prepared by dissolvingthe active ingredient in a sterile aqueous solution such asphysiological saline, buffering solution, etc., or by combining powdercompositions to be dissolved before use. Other vehicles can be chosen,as is known in the art, including, but not limited to: balance saltsolution, saline solution, water soluble polyethers such as polyethyeneglycol, polyvinyls, such as polyvinyl alcohol and povidone, cellulosederivatives such as methylcellulose and hydroxypropyl methylcellulose,petroleum derivatives such as mineral oil and white petrolatum, animalfats such as lanolin, polymers of acrylic acid such ascarboxypolymethylene gel, vegetable fats such as peanut oil andpolysaccharides such as dextrans, and glycosaminoglycans such as sodiumhyaluronate. In some embodiments, additives ordinarily used in the eyedrops can be added. Such additives include isotonizing agents (e.g.,sodium chloride, etc.), buffer agent (e.g., boric acid, sodiummonohydrogen phosphate, sodium dihydrogen phosphate, etc.),preservatives (e.g., benzalkonium chloride, benzethonium chloride,chlorobutanol, etc.), thickeners (e.g., saccharide such as lactose,mannitol, maltose, etc.; e.g., hyaluronic acid or its salt such assodium hyaluronate, potassium hyaluronate, etc.; e.g.,mucopolysaccharide such as chondroitin sulfate, etc.; e.g., sodiumpolyacrylate, carboxyvinyl polymer, crosslinked polyacrylate, polyvinylalcohol, polyvinyl pyrrolidone, methyl cellulose, hydroxy propylmethylcellulose, hydroxyethyl cellulose, carboxymethyl cellulose,hydroxy propyl cellulose or other agents known to those skilled in theart).

The subject pharmaceutical compositions are typically formulated toprovide a therapeutically effective amount of a compound as disclosedherein as the active ingredient, or a pharmaceutically acceptable form,salt, ester, prodrug or derivative thereof. Where desired, thepharmaceutical compositions contain a pharmaceutically acceptable form,such as a salt and/or coordination complex thereof, and one or morepharmaceutically acceptable excipients, carriers, including inert soliddiluents and fillers, diluents, including sterile aqueous solution andvarious organic solvents, permeation enhancers, solubilizers andadjuvants.

The subject pharmaceutical compositions can be administered alone or incombination with one or more other agents, which are also typicallyadministered in the form of pharmaceutical compositions. In someembodiments, the subject compounds and other agent(s) can be mixed intoa preparation or both components can be formulated into separatepreparations to use them in combination separately or at the same time.

In some embodiments, the concentration of one or more of the compoundsprovided in the disclosed pharmaceutical compositions is less than about100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%,14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%,0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%,0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%,0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%,0.0003%, 0.0002%, or 0.0001% w/w, w/v or v/v.

In some embodiments, the concentration of one or more of the compoundsas disclosed herein is greater than about 90%, 80%, 70%, 60%, 50%, 40%,30%, 20%, 19.75%, 19.50%, 19.25% 19%, 18.75%, 18.50%, 18.25% 18%,17.75%, 17.50%, 17.25% 17%, 16.75%, 16.50%, 16.25% 16%, 15.75%, 15.50%,15.25% 15%, 14.75%, 14.50%, 14.25% 14%, 13.75%, 13.50%, 13.25% 13%,12.75%, 12.50%, 12.25% 12%, 11.75%, 11.50%, 11.25% 11%, 10.75%, 10.50%,10.25% 10%, 9.75%, 9.50%, 9.25% 9%, 8.75%, 8.50%, 8.25% 8%, 7.75%,7.50%, 7.25% 7%, 6.75%, 6.50%, 6.25% 6%, 5.75%, 5.50%, 5.25% 5%, 4.75%,4.50%, 4.25%, 4%, 3.75%, 3.50%, 3.25%, 3%, 2.75%, 2.50%, 2.25%, 2%,1.75%, 1.50%, 125%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%,0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%,0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%,0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002%, or 0.0001% w/w,w/v, or v/v.

In some embodiments, the concentration of one or more of the compoundsas disclosed herein is in the range from approximately 0.0001% toapproximately 50%, approximately 0.001% to approximately 40%,approximately 0.01% to approximately 30%, approximately 0.02% toapproximately 29%, approximately 0.03% to approximately 28%,approximately 0.04% to approximately 27%, approximately 0.05% toapproximately 26%, approximately 0.06% to approximately 25%,approximately 0.07% to approximately 24%, approximately 0.08% toapproximately 23%, approximately 0.09% to approximately 22%,approximately 0.1% to approximately 21%, approximately 0.2% toapproximately 20%, approximately 0.3% to approximately 19%,approximately 0.4% to approximately 18%, approximately 0.5% toapproximately 17%, approximately 0.6% to approximately 16%,approximately 0.7% to approximately 15%, approximately 0.8% toapproximately 14%, approximately 0.9% to approximately 12%,approximately 1% to approximately 10% w/w, w/v or v/v. v/v.

In some embodiments, the concentration of one or more of the compoundsas disclosed herein is in the range from approximately 0.001% toapproximately 10%, approximately 0.01% to approximately 5%,approximately 0.02% to approximately 4.5%, approximately 0.03% toapproximately 4%, approximately 0.04% to approximately 3.5%,approximately 0.05% to approximately 3%, approximately 0.06% toapproximately 2.5%, approximately 0.07% to approximately 2%,approximately 0.08% to approximately 1.5%, approximately 0.09% toapproximately 1%, approximately 0.1% to approximately 0.9% w/w, w/v orv/v.

In some embodiments, the amount of one or more of the compounds asdisclosed herein is equal to or less than about 10 g, 9.5 g, 9.0 g, 8.5g, 8.0 g, 7.5 g, 7.0 g, 6.5 g, 6.0 g, 5.5 g, 5.0 g, 4.5 g, 4.0 g, 3.5 g,3.0 g, 2.5 g, 2.0 g, 1.5 g, 1.0 g, 0.95 g, 0.9 g, 0.85 g, 0.8 g, 0.75 g,0.7 g, 0.65 g, 0.6 g, 0.55 g, 0.5 g, 0.45 g, 0.4 g, 0.35 g, 0.3 g, 0.25g, 0.2 g, 0.15 g, 0.1 g, 0.09 g, 0.08 g, 0.07 g, 0.06 g, 0.05 g, 0.04 g,0.03 g, 0.02 g, 0.01 g, 0.009 g, 0.008 g, 0.007 g, 0.006 g, 0.005 g,0.004 g, 0.003 g, 0.002 g, 0.001 g, 0.0009 g, 0.0008 g, 0.0007 g, 0.0006g, 0.0005 g, 0.0004 g, 0.0003 g, 0.0002 g, or 0.0001 g.

In some embodiments, the amount of one or more of the compounds asdisclosed herein is more than about 0.0001 g, 0.0002 g, 0.0003 g, 0.0004g, 0.0005 g, 0.0006 g, 0.0007 g, 0.0008 g, 0.0009 g, 0.001 g, 0.0015 g,0.002 g, 0.0025 g, 0.003 g, 0.0035 g, 0.004 g, 0.0045 g, 0.005 g, 0.0055g, 0.006 g, 0.0065 g, 0.007 g, 0.0075 g, 0.008 g, 0.0085 g, 0.009 g,0.0095 g, 0.01 g, 0.015 g, 0.02 g, 0.025 g, 0.03 g, 0.035 g, 0.04 g,0.045 g, 0.05 g, 0.055 g, 0.06 g, 0.065 g, 0.07 g, 0.075 g, 0.08 g,0.085 g, 0.09 g, 0.095 g, 0.1 g, 0.15 g, 0.2 g, 0.25 g, 0.3 g, 0.35 g,0.4 g, 0.45 g, 0.5 g, 0.55 g, 0.6 g, 0.65 g, 0.7 g, 0.75 g, 0.8 g, 0.85g, 0.9 g, 0.95 g, 1 g, 1.5 g, 2 g, 2.5, 3 g, 3.5, 4 g, 4.5 g, 5 g, 5.5g, 6 g, 6.5 g, 7 g, 7.5 g, 8 g, 8.5 g, 9 g, 9.5 g, or 10 g.

In some embodiments, the amount of one or more of the compounds asdisclosed herein is in the range of about 0.0001-10 g, 0.0005-9 g,0.001-8 g, 0.005-7 g, 0.01-6 g, 0.05-5 g, 0.1-4 g, 0.5-4 g, or 1-3 g.

The compounds as disclosed herein are effective over a wide dosagerange. For example, in the treatment of adult humans, dosages from about0.01 to 1000 mg, from about 0.5 to 100 mg, from about 1 to 50 mg perday, and from about 5 to 40 mg per day are examples of dosages that canbe used. An exemplary dosage is about 10 to 30 mg per day. The exactdosage will depend upon the route of administration, the form in whichthe compound is administered, the subject to be treated, the body weightof the subject to be treated, and the preference and experience of theattending physician.

Described below are non-limiting exemplary pharmaceutical compositionsand methods for preparing the same.

Pharmaceutical compositions for oral administration: In someembodiments, provided herein are pharmaceutical compositions for oraladministration containing a compound as disclosed herein, and apharmaceutical excipient suitable for oral administration.

In some embodiments, provided herein are solid pharmaceuticalcompositions for oral administration containing: (i) an effective amountof a disclosed compound; optionally (ii) an effective amount of a secondagent; and (iii) a pharmaceutical excipient suitable for oraladministration. In some embodiments, the pharmaceutical compositionfurther contains: (iv) an effective amount of a third agent.

In some embodiments, the pharmaceutical composition can be a liquidpharmaceutical composition suitable for oral consumption. Pharmaceuticalcompositions suitable for oral administration can be presented asdiscrete dosage forms, such as capsules, cachets, or tablets, or liquidsor aerosol sprays each containing a predetermined amount of an activeingredient as a powder or in granules, a solution, or a suspension in anaqueous or non-aqueous liquid, an oil-in-water emulsion, or awater-in-oil liquid emulsion. Such dosage forms can be prepared by anyof the methods of pharmacy, but all methods include the step of bringingthe active ingredient into association with the carrier, whichconstitutes one or more ingredients. In general, the pharmaceuticalcompositions are prepared by uniformly and intimately admixing theactive ingredient with liquid carriers or finely divided solid carriersor both, and then, if necessary, shaping the product into the desiredpresentation. For example, a tablet can be prepared by compression ormolding, optionally with one or more accessory ingredients. Compressedtablets can be prepared by compressing in a suitable machine the activeingredient in a free-flowing form such as powder or granules, optionallymixed with an excipient such as, but not limited to, a binder, alubricant, an inert diluent, and/or a surface active or dispersingagent. Molded tablets can be made by molding in a suitable machine amixture of the powdered compound moistened with an inert liquid diluent.

The present disclosure further encompasses anhydrous pharmaceuticalcompositions and dosage forms comprising an active ingredient, sincewater can facilitate the degradation of some compounds. For example,water can be added (e.g., about 5%) in the pharmaceutical arts as ameans of simulating long-term storage in order to determinecharacteristics such as shelf-life or the stability of formulations overtime. Anhydrous pharmaceutical compositions and dosage forms can beprepared using anhydrous or low moisture containing ingredients and lowmoisture or low humidity conditions. For example, pharmaceuticalcompositions and dosage forms which contain lactose can be madeanhydrous if substantial contact with moisture and/or humidity duringmanufacturing, packaging, and/or storage is expected. An anhydrouspharmaceutical composition can be prepared and stored such that itsanhydrous nature is maintained. Accordingly, anhydrous pharmaceuticalcompositions can be packaged using materials known to prevent exposureto water such that they can be included in suitable formulary kits.Examples of suitable packaging include, but are not limited to,hermetically sealed foils, plastic or the like, unit dose containers,blister packs, and strip packs.

An active ingredient can be combined in an intimate admixture with apharmaceutical carrier according to conventional pharmaceuticalcompounding techniques. The carrier can take a wide variety of formsdepending on the form of preparation desired for administration. Inpreparing the pharmaceutical compositions for an oral dosage form, anyof the usual pharmaceutical media can be employed as carriers, such as,for example, water, glycols, oils, alcohols, flavoring agents,preservatives, coloring agents, and the like in the case of oral liquidpreparations (such as suspensions, solutions, and elixirs) or aerosols;or carriers such as starches, sugars, micro-crystalline cellulose,diluents, granulating agents, lubricants, binders, and disintegratingagents can be used in the case of oral solid preparations, in someembodiments without employing the use of lactose. For example, suitablecarriers include powders, capsules, and tablets, with the solid oralpreparations. In some embodiments, tablets can be coated by standardaqueous or nonaqueous techniques.

Binders suitable for use in pharmaceutical compositions and dosage formsinclude, but are not limited to, corn starch, potato starch, or otherstarches, gelatin, natural and synthetic gums such as acacia, sodiumalginate, alginic acid, other alginates, powdered tragacanth, guar gum,cellulose and its derivatives (e.g., ethyl cellulose, cellulose acetate,carboxymethyl cellulose calcium, sodium carboxymethyl cellulose),polyvinyl pyrrolidone, methyl cellulose, pre-gelatinized starch,hydroxypropyl methyl cellulose, microcrystalline cellulose, and mixturesthereof.

Examples of suitable fillers for use in the pharmaceutical compositionsand dosage forms disclosed herein include, but are not limited to, talc,calcium carbonate (e.g., granules or powder), microcrystallinecellulose, powdered cellulose, dextrates, kaolin, mannitol, silicicacid, sorbitol, starch, pre-gelatinized starch, and mixtures thereof.

Disintegrants can be used in the pharmaceutical compositions as providedherein to provide tablets that disintegrate when exposed to an aqueousenvironment. Too much of a disintegrant can produce tablets which candisintegrate in the bottle. Too little may be insufficient fordisintegration to occur and can thus alter the rate and extent ofrelease of the active ingredient(s) from the dosage form. Thus, asufficient amount of disintegrant that is neither too little nor toomuch to detrimentally alter the release of the active ingredient(s) canbe used to form the dosage forms of the compounds disclosed herein. Theamount of disintegrant used can vary based upon the type of formulationand mode of administration, and can be readily discernible to those ofordinary skill in the art. About 0.5 to about 15 weight percent ofdisintegrant, or about 1 to about 5 weight percent of disintegrant, canbe used in the pharmaceutical composition. Disintegrants that can beused to form pharmaceutical compositions and dosage forms include, butare not limited to, agar-agar, alginic acid, calcium carbonate,microcrystalline cellulose, croscarmellose sodium, crospovidone,polacrilin potassium, sodium starch glycolate, potato or tapioca starch,other starches, pre-gelatinized starch, other starches, clays, otheralgins, other celluloses, gums or mixtures thereof.

Lubricants which can be used to form pharmaceutical compositions anddosage forms include, but are not limited to, calcium stearate,magnesium stearate, mineral oil, light mineral oil, glycerin, sorbitol,mannitol, polyethylene glycol, other glycols, stearic acid, sodiumlauryl sulfate, talc, hydrogenated vegetable oil (e.g., peanut oil,cottonseed oil, sunflower oil, sesame oil, olive oil, corn oil, andsoybean oil), zinc stearate, ethyl oleate, ethylaureate, agar, ormixtures thereof. Additional lubricants include, for example, a syloidsilica gel, a coagulated aerosol of synthetic silica, or mixturesthereof. A lubricant can optionally be added, in an amount of less thanabout 1 weight percent of the pharmaceutical composition.

When aqueous suspensions and/or elixirs are desired for oraladministration, the active ingredient therein can be combined withvarious sweetening or flavoring agents, coloring matter or dyes and, forexample, emulsifying and/or suspending agents, together with suchdiluents as water, ethanol, propylene glycol, glycerin and variouscombinations thereof.

The tablets can be uncoated or coated by known techniques to delaydisintegration and absorption in the gastrointestinal tract and therebyprovide a sustained action over a longer period. For example, a timedelay material such as glyceryl monostearate or glyceryl distearate canbe employed. Formulations for oral use can also be presented as hardgelatin capsules wherein the active ingredient is mixed with an inertsolid diluent, for example, calcium carbonate, calcium phosphate orkaolin, or as soft gelatin capsules wherein the active ingredient ismixed with water or an oil medium, for example, peanut oil, liquidparaffin or olive oil.

Surfactant which can be used to form pharmaceutical compositions anddosage forms include, but are not limited to, hydrophilic surfactants,lipophilic surfactants, and mixtures thereof. That is, a mixture ofhydrophilic surfactants can be employed, a mixture of lipophilicsurfactants can be employed, or a mixture of at least one hydrophilicsurfactant and at least one lipophilic surfactant can be employed.

A suitable hydrophilic surfactant can generally have an HLB value of atleast about 10, while suitable lipophilic surfactants can generally havean HLB value of or less than about 10. An empirical parameter used tocharacterize the relative hydrophilicity and hydrophobicity of non-ionicamphiphilic compounds is the hydrophilic-lipophilic balance (“HLB”value). Surfactants with lower HLB values are more lipophilic orhydrophobic, and have greater solubility in oils, while surfactants withhigher HLB values are more hydrophilic, and have greater solubility inaqueous solutions. Hydrophilic surfactants are generally considered tobe those compounds having an HLB value greater than about 10, as well asanionic, cationic, or zwitterionic compounds for which the HLB scale isnot generally applicable. Similarly, lipophilic (i.e., hydrophobic)surfactants are compounds having an HLB value equal to or less thanabout 10. However, HLB value of a surfactant is merely a rough guidegenerally used to enable formulation of industrial, pharmaceutical andcosmetic emulsions.

Hydrophilic surfactants can be either ionic or non-ionic. Suitable ionicsurfactants include, but are not limited to, alkylammonium salts;fusidic acid salts; fatty acid derivatives of amino acids,oligopeptides, and polypeptides; glyceride derivatives of amino acids,oligopeptides, and polypeptides; lecithins and hydrogenated lecithins;lysolecithins and hydrogenated lysolecithins; phospholipids andderivatives thereof; lysophospholipids and derivatives thereof;carnitine fatty acid ester salts; salts of alkylsulfates; fatty acidsalts; sodium docusate; acylactylates; mono- and di-acetylated tartaricacid esters of mono- and di-glycerides; succinylated mono- anddi-glycerides; citric acid esters of mono- and di-glycerides; andmixtures thereof.

Within the aforementioned group, ionic surfactants include, by way ofexample: lecithins, lysolecithin, phospholipids, lysophospholipids andderivatives thereof; carnitine fatty acid ester salts; salts ofalkylsulfates; fatty acid salts; sodium docusate; acylactylates; mono-and di-acetylated tartaric acid esters of mono- and di-glycerides;succinylated mono- and di-glycerides; citric acid esters of mono- anddi-glycerides; and mixtures thereof.

Ionic surfactants can be the ionized forms of lecithin, lysolecithin,phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol,phosphatidic acid, phosphatidylserine, lysophosphatidylcholine,lysophosphatidylethanolamine, lysophosphatidylglycerol, lysophosphatidicacid, lysophosphatidylserine, PEG-phosphatidylethanolamine,PVP-phosphatidylethanolamine, lactylic esters of fatty acids,stearoyl-2-lactylate, stearoyl lactylate, succinylated monoglycerides,mono/diacetylated tartaric acid esters of mono/diglycerides, citric acidesters of mono/diglycerides, cholylsarcosine, caproate, caprylate,caprate, laurate, myristate, palmitate, oleate, ricinoleate, linoleate,linolenate, stearate, lauryl sulfate, teracecyl sulfate, docusate,lauroyl carnitines, palmitoyl carnitines, myristoyl carnitines, andsalts and mixtures thereof.

Hydrophilic non-ionic surfactants can include, but are not limited to,alkylglucosides; alkylmaltosides; alkylthioglucosides; laurylmacrogolglycerides; polyoxyalkylene alkyl ethers such as polyethyleneglycol alkyl ethers; polyoxyalkylene alkylphenols such as polyethyleneglycol alkyl phenols; polyoxyalkylene alkyl phenol fatty acid esterssuch as polyethylene glycol fatty acids monoesters and polyethyleneglycol fatty acids diesters; polyethylene glycol glycerol fatty acidesters; polyglycerol fatty acid esters; polyoxyalkylene sorbitan fattyacid esters such as polyethylene glycol sorbitan fatty acid esters;hydrophilic transesterification products of a polyol with at least onemember of glycerides, vegetable oils, hydrogenated vegetable oils, fattyacids, and sterols; polyoxyethylene sterols, derivatives, and analoguesthereof; polyoxyethylated vitamins and derivatives thereof;polyoxyethylene-polyoxypropylene block copolymers; and mixtures thereof;polyethylene glycol sorbitan fatty acid esters and hydrophilictransesterification products of a polyol with at least one member oftriglycerides, vegetable oils, and hydrogenated vegetable oils. Thepolyol can be glycerol, ethylene glycol, polyethylene glycol, sorbitol,propylene glycol, pentaerythritol, or a saccharide.

Other hydrophilic-non-ionic surfactants include, without limitation,PEG-10 laurate, PEG-12 laurate, PEG-20 laurate, PEG-32 laurate, PEG-32dilaurate, PEG-12 oleate, PEG-15 oleate, PEG-20 oleate, PEG-20 dioleate,PEG-32 oleate, PEG-200 oleate, PEG-400 oleate, PEG-15 stearate, PEG-32distearate, PEG-40 stearate, PEG-100 stearate, PEG-20 dilaurate, PEG-25glyceryl trioleate, PEG-32 dioleate, PEG-20 glyceryl laurate, PEG-30glyceryl laurate, PEG-20 glyceryl stearate, PEG-20 glyceryl oleate,PEG-30 glyceryl oleate, PEG-30 glyceryl laurate, PEG-40 glyceryllaurate, PEG-40 palm kernel oil, PEG-50 hydrogenated castor oil, PEG-40castor oil, PEG-35 castor oil, PEG-60 castor oil, PEG-40 hydrogenatedcastor oil, PEG-60 hydrogenated castor oil, PEG-60 corn oil, PEG-6caprate/caprylate glycerides, PEG-8 caprate/caprylate glycerides,polyglyceryl-10 laurate, PEG-30 cholesterol, PEG-25 phyto sterol, PEG-30soya sterol, PEG-20 trioleate, PEG-40 sorbitan oleate, PEG-80 sorbitanlaurate, polysorbate 20, polysorbate 80, POE-9 lauryl ether, POE-23lauryl ether, POE-10 oleyl ether, POE-20 oleyl ether, POE-20 stearylether, tocopheryl PEG-100 succinate, PEG-24 cholesterol, polyglyceryl-10oleate, Tween 40, Tween 60, sucrose monostearate, sucrose monolaurate,sucrose monopalmitate, PEG 10-100 nonyl phenol series, PEG 15-100 octylphenol series, and poloxamers.

Suitable lipophilic surfactants include, by way of example only: fattyalcohols; glycerol fatty acid esters; acetylated glycerol fatty acidesters; lower alcohol fatty acids esters; propylene glycol fatty acidesters; sorbitan fatty acid esters; polyethylene glycol sorbitan fattyacid esters; sterols and sterol derivatives; polyoxyethylated sterolsand sterol derivatives; polyethylene glycol alkyl ethers; sugar esters;sugar ethers; lactic acid derivatives of mono- and di-glycerides;hydrophobic transesterification products of a polyol with at least onemember of glycerides, vegetable oils, hydrogenated vegetable oils, fattyacids and sterols; oil-soluble vitamins/vitamin derivatives; andmixtures thereof. Within this group, non-limiting examples of lipophilicsurfactants include glycerol fatty acid esters, propylene glycol fattyacid esters, and mixtures thereof, or are hydrophobictransesterification products of a polyol with at least one member ofvegetable oils, hydrogenated vegetable oils, and triglycerides.

In one embodiment, the pharmaceutical composition can include asolubilizer to ensure good solubilization and/or dissolution of acompound as provided herein and to minimize precipitation of thecompound. This can be especially important for pharmaceuticalcompositions for non-oral use, e.g., pharmaceutical compositions forinjection. A solubilizer can also be added to increase the solubility ofthe hydrophilic drug and/or other components, such as surfactants, or tomaintain the pharmaceutical composition as a stable or homogeneoussolution or dispersion.

Examples of suitable solubilizers include, but are not limited to, thefollowing: alcohols and polyols, such as ethanol, isopropanol, butanol,benzyl alcohol, ethylene glycol, propylene glycol, butanediols andisomers thereof, glycerol, pentaerythritol, sorbitol, mannitol,transcutol, dimethyl isosorbide, polyethylene glycol, polypropyleneglycol, polyvinylalcohol, hydroxypropyl methylcellulose and othercellulose derivatives, cyclodextrins and cyclodextrin derivatives;ethers of polyethylene glycols having an average molecular weight ofabout 200 to about 6000, such as tetrahydrofurfuryl alcohol PEG ether(glycofurol) or methoxy PEG; amides and other nitrogen-containingcompounds such as 2-pyrrolidone, 2-piperidone, ε-caprolactam,N-alkylpyrrolidone, N-hydroxyalkylpyrrolidone, N-alkylpiperidone,N-alkylcaprolactam, dimethylacetamide and polyvinylpyrrolidone; esterssuch as ethyl propionate, tributylcitrate, acetyl triethylcitrate,acetyl tributyl citrate, triethylcitrate, ethyl oleate, ethyl caprylate,ethyl butyrate, triacetin, propylene glycol monoacetate, propyleneglycol diacetate, ε-caprolactone and isomers thereof, δ-valerolactoneand isomers thereof, β-butyrolactone and isomers thereof; and othersolubilizers known in the art, such as dimethyl acetamide, dimethylisosorbide, N-methylpyrrolidones, monooctanoin, diethylene glycolmonoethyl ether, and water.

Mixtures of solubilizers can also be used. Examples include, but notlimited to, triacetin, triethylcitrate, ethyl oleate, ethyl caprylate,dimethylacetamide, N-methylpyrrolidone, N-hydroxyethylpyrrolidone,polyvinylpyrrolidone, hydroxypropyl methylcellulose, hydroxypropylcyclodextrins, ethanol, polyethylene glycol 200-100, glycofurol,transcutol, propylene glycol, and dimethyl isosorbide. In someembodiments, solubilizers include sorbitol, glycerol, triacetin, ethylalcohol, PEG-400, glycofurol and propylene glycol.

The amount of solubilizer that can be included is not particularlylimited. The amount of a given solubilizer can be limited to abioacceptable amount, which can be readily determined by one of skill inthe art. In some circumstances, it can be advantageous to includeamounts of solubilizers far in excess of bioacceptable amounts, forexample to maximize the concentration of the drug, with excesssolubilizer removed prior to providing the pharmaceutical composition toa subject using conventional techniques, such as distillation orevaporation. Thus, if present, the solubilizer can be in a weight ratioof about 10%, 25%, 50%, 100%, or up to about 200% by weight, based onthe combined weight of the drug, and other excipients. If desired, verysmall amounts of solubilizer can also be used, such as about 5%, 2%, 1%or even less. Typically, the solubilizer can be present in an amount ofabout 1% to about 100%, more typically about 5% to about 25% by weight.

The pharmaceutical composition can further include one or morepharmaceutically acceptable additives and excipients. Such additives andexcipients include, without limitation, detackifiers, anti-foamingagents, buffering agents, polymers, antioxidants, preservatives,chelating agents, viscomodulators, tonicifiers, flavorants, colorants,odorants, opacifiers, suspending agents, binders, fillers, plasticizers,lubricants, and mixtures thereof.

In addition, an acid or a base can be incorporated into thepharmaceutical composition to facilitate processing, to enhancestability, or for other reasons. Examples of pharmaceutically acceptablebases include amino acids, amino acid esters, ammonium hydroxide,potassium hydroxide, sodium hydroxide, sodium hydrogen carbonate,aluminum hydroxide, calcium carbonate, magnesium hydroxide, magnesiumaluminum silicate, synthetic aluminum silicate, synthetic hydrocalcite,magnesium aluminum hydroxide, diisopropylethylamine, ethanolamine,ethylenediamine, triethanolamine, triethylamine, triisopropanolamine,trimethylamine, tris(hydroxymethyl)aminomethane (TRIS) and the like.Also suitable are bases that are salts of a pharmaceutically acceptableacid, such as acetic acid, acrylic acid, adipic acid, alginic acid,alkanesulfonic acid, amino acids, ascorbic acid, benzoic acid, boricacid, butyric acid, carbonic acid, citric acid, fatty acids, formicacid, fumaric acid, gluconic acid, hydroquinosulfonic acid, isoascorbicacid, lactic acid, maleic acid, oxalic acid, para-bromophenylsulfonicacid, propionic acid, p-toluenesulfonic acid, salicylic acid, stearicacid, succinic acid, tannic acid, tartaric acid, thioglycolic acid,toluenesulfonic acid, uric acid, and the like. Salts of polyproticacids, such as sodium phosphate, disodium hydrogen phosphate, and sodiumdihydrogen phosphate can also be used. When the base is a salt, thecation can be any convenient and pharmaceutically acceptable cation,such as ammonium, alkali metals, alkaline earth metals, and the like.Examples can include, but not limited to, sodium, potassium, lithium,magnesium, calcium and ammonium.

Suitable acids are pharmaceutically acceptable organic or inorganicacids. Examples of suitable inorganic acids include hydrochloric acid,hydrobromic acid, hydriodic acid, sulfuric acid, nitric acid, boricacid, phosphoric acid, and the like. Examples of suitable organic acidsinclude acetic acid, acrylic acid, adipic acid, alginic acid,alkanesulfonic acids, amino acids, ascorbic acid, benzoic acid, boricacid, butyric acid, carbonic acid, citric acid, fatty acids, formicacid, fumaric acid, gluconic acid, hydroquinosulfonic acid, isoascorbicacid, lactic acid, maleic acid, methanesulfonic acid, oxalic acid,para-bromophenylsulfonic acid, propionic acid, p-toluenesulfonic acid,salicylic acid, stearic acid, succinic acid, tannic acid, tartaric acid,thioglycolic acid, toluenesulfonic acid, uric acid and the like.

Pharmaceutical compositions for injection. In some embodiments, providedherein are pharmaceutical compositions for injection containing acompound gas disclosed herein and a pharmaceutical excipient suitablefor injection. Components and amounts of agents in the pharmaceuticalcompositions are as described herein.

The forms in which the disclosed pharmaceutical compositions can beincorporated for administration by injection include aqueous or oilsuspensions, or emulsions, with sesame oil, corn oil, cottonseed oil, orpeanut oil, as well as elixirs, mannitol, dextrose, or a sterile aqueoussolution, and similar pharmaceutical vehicles.

Aqueous solutions in saline are also conventionally used for injection.Ethanol, glycerol, propylene glycol, liquid polyethylene glycol, and thelike (and suitable mixtures thereof), cyclodextrin derivatives, andvegetable oils can also be employed. The proper fluidity can bemaintained, for example, by the use of a coating, such as lecithin, forthe maintenance of the required particle size in the case of dispersionand by the use of surfactants. The prevention of the action ofmicroorganisms can be brought about by various antibacterial andantifungal agents, for example, parabens, chlorobutanol, phenol, sorbicacid, thimerosal, and the like.

Sterile injectable solutions are prepared by incorporating a compound asdisclosed herein in the required amount in the appropriate solvent withvarious other ingredients as enumerated above, as appropriate, followedby filtered sterilization. Generally, dispersions are prepared byincorporating the various sterilized active ingredients into a sterilevehicle which contains the basic dispersion medium and the appropriateother ingredients from those enumerated above. In the case of sterilepowders for the preparation of sterile injectable solutions, certainmethods of preparation are vacuum-drying and freeze-drying techniqueswhich yield a powder of the active ingredient plus any additionalingredient from a previously sterile-filtered solution thereof.

Pharmaceutical compositions for topical (e.g., transdermal) delivery. Insome embodiments, provided herein are pharmaceutical compositions fortransdermal delivery containing a compound as disclosed herein and apharmaceutical excipient suitable for transdermal delivery.

Pharmaceutical compositions provided herein can be formulated intopreparations in solid, semi-solid, or liquid forms suitable for local ortopical administration, such as gels, water soluble jellies, creams,lotions, suspensions, foams, powders, slurries, ointments, solutions,oils, pastes, suppositories, sprays, emulsions, saline solutions,dimethylsulfoxide (DMSO)-based solutions. In general, carriers withhigher densities are capable of providing an area with a prolongedexposure to the active ingredients. In contrast, a solution formulationcan provide more immediate exposure of the active ingredient to thechosen area.

The pharmaceutical compositions also can comprise suitable solid or gelphase carriers or excipients, which are compounds that allow increasedpenetration of, or assist in the delivery of, therapeutic moleculesacross the stratum corneum permeability barrier of the skin. There aremany of these penetration-enhancing molecules known to those trained inthe art of topical formulation. Examples of such carriers and excipientsinclude, but are not limited to, humectants (e.g., urea), glycols (e.g.,propylene glycol), alcohols (e.g., ethanol), fatty acids (e.g., oleicacid), surfactants (e.g., isopropyl myristate and sodium laurylsulfate), pyrrolidones, glycerol monolaurate, sulfoxides, terpenes(e.g., menthol), amines, amides, alkanes, alkanols, water, calciumcarbonate, calcium phosphate, various sugars, starches, cellulosederivatives, gelatin, and polymers such as polyethylene glycols.

Another exemplary formulation for use in the disclosed methods employstransdermal delivery devices (“patches”). Such transdermal patches canbe used to provide continuous or discontinuous infusion of a compound asprovided herein in controlled amounts, either with or without anotheragent.

The construction and use of transdermal patches for the delivery ofpharmaceutical agents is well known in the art. See, e.g., U.S. Pat.Nos. 5,023,252, 4,992,445 and 5,001,139. Such patches can be constructedfor continuous, pulsatile, or on demand delivery of pharmaceuticalagents.

Pharmaceutical compositions for inhalation. Pharmaceutical compositionsfor inhalation or insufflation include solutions and suspensions inpharmaceutically acceptable, aqueous or organic solvents, or mixturesthereof, and powders. The liquid or solid pharmaceutical compositionscan contain suitable pharmaceutically acceptable excipients as describedherein. In some embodiments, the pharmaceutical compositions areadministered by the oral or nasal respiratory route for local orsystemic effect. Pharmaceutical compositions in pharmaceuticallyacceptable solvents can be nebulized by use of inert gases. Nebulizedsolutions can be inhaled directly from the nebulizing device or thenebulizing device can be attached to a face mask tent, or intermittentpositive pressure breathing machine. Solution, suspension, or powderpharmaceutical compositions can be administered, e.g., orally ornasally, from devices that deliver the formulation in an appropriatemanner.

Pharmaceutical compositions can also be prepared from compositionsdescribed herein and one or more pharmaceutically acceptable excipientssuitable for sublingual, buccal, rectal, intraosseous, intraocular,intranasal, epidural, or intraspinal administration. Preparations forsuch pharmaceutical compositions are well-known in the art. See, e.g.,Anderson, Philip O.; Knoben, James E.; Troutman, William G, eds.,Handbook of Clinical Drug Data, Tenth Edition, McGraw-Hill, 2002; Prattand Taylor, eds., Principles of Drug Action, Third Edition, ChurchillLivingston, New York, 1990; Katzung, ed., Basic and ClinicalPharmacology, Ninth Edition, McGraw Hill, 20037ybg; Goodman and Gilman,eds., The Pharmacological Basis of Therapeutics, Tenth Edition, McGrawHill, 2001; Remingtons Pharmaceutical Sciences, 20th Ed., LippincottWilliams & Wilkins., 2000; Martindale, The Extra Pharmacopoeia,Thirty-Second Edition (The Pharmaceutical Press, London, 1999); all ofwhich are incorporated by reference herein in their entirety.

Administration of the compounds or pharmaceutical compositions asdisclosed herein can be effected by any method that enables delivery ofthe compounds to the site of action. These methods include oral routes,intraduodenal routes, parenteral injection (including intravenous,intraarterial, subcutaneous, intramuscular, intravascular,intraperitoneal or infusion), topical (e.g., transdermal application),rectal administration, via local delivery by catheter or stent orthrough inhalation. Compounds can also be administered intraadiposallyor intrathecally.

The amount of the compound administered will be dependent on the subjectbeing treated, the severity of the disorder or condition, the rate ofadministration, the disposition of the compound and the discretion ofthe prescribing physician. However, an effective dosage can be in therange of about 0.001 to about 100 mg per kg body weight per day, such asfrom about 1 to about 35 mg/kg/day, in single or divided doses. For a 70kg human, this would amount to about 0.05 to about 7 g/day, such asabout 0.05 to about 2.5 g/day. In some instances, dosage levels belowthe lower limit of the aforesaid range can be more than adequate, whilein other cases still larger doses can be employed without causing anyharmful side effect, e.g., by dividing such larger doses into severalsmall doses for administration throughout the day.

In some embodiments, a compound as provided herein is administered in asingle dose. Typically, such administration will be by injection, e.g.,intravenous injection, in order to introduce the agent quickly. However,other routes can be used as appropriate. A single dose of a compound asprovided herein can also be used for treatment of an acute condition.

In some embodiments, a compound as provided herein is administered inmultiple doses. Dosing can be about once, twice, three times, fourtimes, five times, six times, or more than six times per day. Dosing canbe about once a month, once every two weeks, once a week, or once everyother day. In another embodiment, a compound as disclosed herein andanother agent are administered together about once per day to about 6times per day. In another embodiment, the administration of a compoundas provided herein and an agent continues for less than about 7 days. Inyet another embodiment, the administration continues for more than about6, 10, 14, 28 days, two months, six months, or one year. In some cases,continuous dosing is achieved and maintained as long as necessary.

Administration of the agents as disclosed herein can continue as long asnecessary. In some embodiments, an agent as disclosed herein isadministered for more than 1, 2, 3, 4, 5, 6, 7, 14, or 28 days. In someembodiments, an agent as disclosed herein is administered for less than28, 14, 7, 6, 5, 4, 3, 2, or 1 day. In some embodiments, an agent asdisclosed herein is administered chronically on an ongoing basis, e.g.,for the treatment of chronic effects.

An effective amount of a compound as disclosed herein can beadministered in either single or multiple doses by any of the acceptedmodes of administration of agents having similar utilities, includingrectal, buccal, intranasal and transdermal routes, by intra-arterialinjection, intravenously, intraperitoneally, parenterally,intramuscularly, subcutaneously, orally, topically, or as an inhalant.

The pharmaceutical compositions provided herein can also be deliveredvia an impregnated or coated device such as a stent, for example, or anartery-inserted cylindrical polymer. Such a method of administrationcan, for example, aid in the prevention or amelioration of restenosisfollowing procedures such as balloon angioplasty. Without being bound bytheory, compounds as disclosed herein can slow or inhibit the migrationand proliferation of smooth muscle cells in the arterial wall whichcontribute to restenosis. A compound as disclosed herein can beadministered, for example, by local delivery from the struts of a stent,from a stent graft, from grafts, or from the cover or sheath of a stent.In some embodiments, a compound as disclosed herein is admixed with amatrix. Such a matrix can be a polymeric matrix, and can serve to bondthe compound to the stent. Polymeric matrices suitable for such use,include, for eample, lactone-based polyesters or copolyesters such aspolylactide, polycaprolactonglycolide, polyorthoesters, polyanhydrides,polyaminoacids, polysaccharides, polyphosphazenes, poly (ether-ester)copolymers (e.g., PEO-PLLA); polydimethylsiloxane,poly(ethylene-vinylacetate), acrylate-based polymers or copolymers(e.g., polyhydroxyethyl methylmethacrylate, polyvinyl pyrrolidinone),fluorinated polymers such as polytetrafluoroethylene and celluloseesters. Suitable matrices can be nondegrading or can degrade with time,releasing the compound or compounds. Compounds as disclosed herein canbe applied to the surface of the stent by various methods such asdip/spin coating, spray coating, dip-coating, and/or brush-coating. Thecompounds can be applied in a solvent and the solvent can be allowed toevaporate, thus forming a layer of compound onto the stent.Alternatively, the compound can be located in the body of the stent orgraft, for example in microchannels or micropores. When implanted, thecompound diffuses out of the body of the stent to contact the arterialwall. Such stents can be prepared by dipping a stent manufactured tocontain such micropores or microchannels into a solution of the compoundas disclosed herein in a suitable solvent, followed by evaporation ofthe solvent. Excess drug on the surface of the stent can be removed viaan additional brief solvent wash. In yet other embodiments, compounds asdisclosed herein can be covalently linked to a stent or graft. Acovalent linker can be used which degrades in vivo, leading to therelease of the compound as disclosed herein. Any bio-labile linkage canbe used for such a purpose, such as ester, amide or anhydride linkages.Compounds provided herein can additionally be administeredintravascularly from a balloon used during angioplasty. Extravascularadministration of the compounds via the pericard or via adventialapplication of formulations provided herein can also be performed todecrease restenosis.

A variety of stent devices which can be used as described are disclosed,for example, in the following references, all of which are herebyincorporated by reference: U.S. Pat. No. 5,451,233; U.S. Pat. No.5,040,548; U.S. Pat. No. 5,061,273; U.S. Pat. No. 5,496,346; U.S. Pat.No. 5,292,331; U.S. Pat. No. 5,674,278; U.S. Pat. No. 3,657,744; U.S.Pat. No. 4,739,762; U.S. Pat. No. 5,195,984; U.S. Pat. No. 5,292,331;U.S. Pat. No. 5,674,278; U.S. Pat. No. 5,879,382; U.S. Pat. No.6,344,053.

The compounds provided herein can be administered in dosages. It isknown in the art that due to intersubject variability in compoundpharmacokinetics, individualization of dosing regimen is necessary foroptimal therapy. Dosing for a compound provided herein can be found byroutine experimentation in light of the instant disclosure.

When a compound provided herein, is administered in a pharmaceuticalcomposition that comprises one or more agents, and the agent has ashorter half-life than the compound provided herein unit dose forms ofthe agent and the compound provided herein can be adjusted accordingly.

The subject pharmaceutical composition can, for example, be in a formsuitable for oral administration as a tablet, capsule, pill, powder,sustained release formulations, solution, or suspension, for parenteralinjection as a sterile solution, suspension or emulsion, for topicaladministration as an ointment or cream or for rectal administration as asuppository. The pharmaceutical composition can be in unit dosage formssuitable for single administration of precise dosages. Thepharmaceutical composition will include a conventional pharmaceuticalcarrier or excipient and a compound as provided herein as an activeingredient. In addition, it can include other medicinal orpharmaceutical agents, carriers, adjuvants, etc.

Exemplary parenteral administration forms include solutions orsuspensions of active compound in sterile aqueous solutions, forexample, aqueous propylene glycol or dextrose solutions. Such dosageforms can be suitably buffered, if desired.

In some embodiments, provided herein are kits. The kits include acompound or compounds as described herein, in suitable packaging, andwritten material that can include instructions for use, discussion ofclinical studies, listing of side effects, and the like. Such kits canalso include information, such as scientific literature references,package insert materials, clinical trial results, and/or summaries ofthese and the like, which indicate or establish the activities and/oradvantages of the pharmaceutical composition, and/or which describedosing, administration, side effects, drug interactions, or otherinformation useful to the health care provider. Such information can bebased on the results of various studies, for example, studies usingexperimental animals involving in vivo models and studies based on humanclinical trials. The kit can further contain another agent. In someembodiments, the compound as disclosed herein and the agent are providedas separate pharmaceutical compositions in separate containers withinthe kit. In some embodiments, the compound as disclosed herein and theagent are provided as a single pharmaceutical composition within acontainer in the kit. Suitable packaging and additional articles for use(e.g., measuring cup for liquid preparations, foil wrapping to minimizeexposure to air, and the like) are known in the art and can be includedin the kit. Kits described herein can be provided, marketed and/orpromoted to health providers, including physicians, nurses, pharmacists,formulary officials, and the like. Kits can also, in some embodiments,be marketed directly to the consumer.

Phosphoinositide 3-kinases (PI3Ks) are members of a conserved family oflipid kinases that regulate numerous cell functions, includingproliferation, differentiation, cell survival and metabolism. Severalclasses of PI3Ks exist in mammalian cells, including Class IA subgroup(e.g., PI3K-α, β, δ), which are generally activated by receptor tyrosinekinases (RTKs); Class IB (e.g., PI3K-γ), which is activated by G-proteincoupled receptors, among others. PI3Ks exert their biological activitiesvia a “PI3K-mediated signaling pathway” that includes several componentsthat directly and/or indirectly transduce a signal triggered by a PI3K,including the generation of secondary messenger phophotidylinositol,3,4,5-triphosphate (PIP3) at the plasma membrane, activation ofheterotrimeric G protein signaling, and generation of further secondmessengers such as cAMP, DAG, and IP3, all of which leads to anextensive cascade of protein kinase activation (reviewed inVanhaesebroeck, B. et al. (2001) Annu Rev Biochem. 70:535-602). Forexample, PI3K-δ is activated by cellular receptors through interactionbetween the PI3K regulatory subunit (p85) SH2 domains, or through directinteraction with RAS. PIP3 produced by PI3K activates effector pathwaysdownstream through interaction with plextrin homology (PH) domaincontaining enzymes (e.g., PDK-1 and AKT [PKB]). (Fung-Leung W P. (2011)Cell Signal. 23(4):603-8). Unlike PI3K-δ, PI3K-γ is not a Class 1A PI3K,and is not associated with a regulatory subunit of the P85 family, butrather with a regulatory subunit in the p101 family. PI3K-γ isassociated with G-protein coupled receptors (GPCRs), and is responsiblefor the very rapid induction of PIP3, and can be also activated by RAS.

As used herein, a “PI3K-mediated disorder” refers to a disease orcondition involving aberrant PI3K-mediated signaling pathway. In oneembodiment, provided herein is a method of treating a PI3K mediateddisorder in a subject, the method comprising administering atherapeutically effective amount of a compound or a pharmaceuticalcomposition as disclosed herein. In some embodiments, provided herein isa method of treating a PI3K-δ or PI3K-γ mediated disorder in a subject,the method comprising administering a therapeutically effective amountof a compound or a pharmaceutical composition as disclosed herein. Insome embodiments, provided herein is a method for inhibiting at leastone of PI3K-δ or PI3K-γ, the method comprising contacting a cellexpressing PI3K in vitro or in vivo with an effective amount of thecompound or composition disclosed herein PI3Ks have been associated witha wide range of conditions, including immunity, cancer and thrombosis(reviewed in Vanhaesebroeck, B. et al. (2010) Current Topics inMicrobiology and Immunology, DOI 10.1007/82_(—)2010_(—)65). For example,Class I PI3Ks, particularly PI3Kγ and PI3Kδ isoforms, are highlyexpressed in leukocytes and have been associated with adaptive andinnate immunity; thus, these PI3Ks are believed to be importantmediators in inflammatory disorders and hematologic malignancies(reviewed in Harris, S J et al. (2009) Curr Opin Investig Drugs10(11):1151-62); Rommel C. et al. (2007) Nat Rev Immunol 7(3):191-201;Durand C A et al. (2009) J Immunol. 183(9):5673-84; Dil N, Marshall A J.(2009) Mol Immunol. 46(10):1970-8; Al-Alwan M M et al. (2007) J Immunol.178(4):2328-35; Zhang T T, et al. (2008) J Allergy Clin Immunol. 2008;122(4):811-819.e2; Srinivasan L, et al. (2009) Cell 139(3):573-86).

Numerous publications support roles of PI3K-δ, PI3K-γ, and PI3K-β in thedifferentiation, maintenance, and activation of immune and malignantcells, as described in more detail below.

The importance of PI3K-δ in the development and function of B-cells issupported from inhibitor studies and genetic models. PI3K-δ is animportant mediator of B-cell receptor (BCR) signaling, and is upstreamof AKT, calcium flux, PLCγ, MAP kinase, P70S6k, and FOXO3a activation.PI3K-δ is also important in IL4R, S1P, and CXCR5 signaling, and has beenshown to modulate responses to toll-like receptors 4 and 9 Inhibitors ofPI3K-δ have shown the importance of PI3K-δ in B-cell development(Marginal zone and B1 cells), B-cell activation, chemotaxis, migrationand homing to lymphoid tissue, and in the control of immunoglobulinclass switching leading to the production of IgE. Clayton E et al.(2002) J Exp Med. 196(6):753-63; Bilancio A, et al. (2006) Blood107(2):642-50; Okkenhaug K. et al. (2002) Science 297(5583):1031-4;Al-Alwan M M et al. (2007) J Immunol. 178(4):2328-35; Zhang T T, et al.(2008) J Allergy Clin Immunol. 2008; 122(4):811-819.e2; Srinivasan L, etal. (2009) Cell 139(3):573-86)

In T-cells, PI3K-δ has been demonstrated to have a role in T-cellreceptor and cytokine signaling, and is upstream of AKT, PLCγ, andGSK3b. In PI3K-δ deletion or kinase-dead knock-in mice, or in inhibitorstudies, T-cell defects including proliferation, activation, anddifferentiation have been observed, leading to reduced T helper cell 2(TH2) response, memory T-cell specific defects (DTH reduction), defectsin antigen dependent cellular trafficking, and defects inchemotaxis/migration to chemokines (e.g., S1P, CCR7, CD62L). (Garçon F.et al. (2008) Blood 111(3):1464-71; Okkenhaug K et al. (2006). JImmunol. 177(8):5122-8; Soond D R, et al. (2010) Blood 115(11):2203-13;Reif K, (2004). J Immunol. 2004; 173(4):2236-40; Ji H. et al. (2007)Blood 110(8):2940-7; Webb L M, et al. (2005) J Immunol. 175(5):2783-7;Liu D, et al. (2010) J Immunol. 184(6):3098-105; Haylock-Jacobs S, etal. (2011) J Autoimmun. 2011; 36(3-4):278-87; Jarmin S J, et al. (2008)J Clin Invest. 118(3):1154-64).

In neutrophils, PI3K-δ along with PI3K-γ, and PI3K-β, contribute to theresponses to immune complexes, FCgRII signaling, including migration andneutrophil respiratory burst. Human neutrophils undergo rapid inductionof PIP3 in response to formyl peptide receptor (FMLP) or complementcomponent C5a (C5a) in a PI3K-γ dependent manner, followed by a longerPIP3 production period that is PI3K-δ dependent, and is essential forrespiratory burst. The response to immune complexes is contributed byPI3K-δ, PI3K-γ, and PI3K-β, and is an important mediator of tissuedamage in models of autoimmune disease (Randis T M et al. (2008) Eur JImmunol. 38(5):1215-24; Pinho V, (2007) J Immunol. 179(11):7891-8; SadhuC. et al. (2003) J Immunol. 170(5):2647-54; Condliffe A M et al. (2005)Blood 106(4):1432-40).

In macrophages collected from patients with chronic obstructivepulmonary disease (COPD), glucocorticoid responsiveness can be restoredby treatment of the cells with inhibitors of PI3K-δ. Macrophages alsorely on PI3K-δ and PI3K-γ for responses to immune complexes through thearthus reaction (FCgR and C5a signaling) (Randis T M, et al. (2008) EurJ Immunol. 38(5):1215-24; Marwick J A et al. (2009) Am J Respir CritCare Med. 179(7):542-8; Konrad S, et al. (2008) J Biol Chem.283(48):33296-303).

In mast cells, stem cell factor-(SCF) and IL3-dependent proliferation,differentiation and function are PI3K-δ dependent, as is chemotaxis. Theallergen/IgE crosslinking of FCgR1 resulting in cytokine release anddegranulation of the mast cells is severely inhibited by treatment withPI3K-δ inhibitors, suggesting a role for PI3K-δ in allergic disease (AliK et al. (2004) Nature 431(7011):1007-11; Lee K S, et al. (2006) FASEBJ. 20(3):455-65; Kim M S, et al. (2008) Trends Immunol. 29(10):493-501).

Natural killer (NK) cells are dependent on both PI3K-δ and PI3K-γ forefficient migration towards chemokines including CXCL10, CCL3, S1P andCXCL12, or in response to LPS in the peritoneum (Guo H, et al. (2008) JExp Med. 205(10):2419-35; Tassi I, et al. (2007) Immunity 27(2):214-27;Saudemont A, (2009) Proc Natl Acad Sci USA. 106(14):5795-800; Kim N, etal. (2007) Blood 110(9):3202-8).

The roles of PI3K-δ, PI3K-γ, and PI3K-β in the differentiation,maintenance, and activation of immune cells support a role for theseenzymes in inflammatory disorders ranging from autoimmune diseases(e.g., rheumatoid arthritis, multiple sclerosis) to allergicinflammatory disorders, such as asthma and COPD. Extensive evidence isavailable in experimental animal models, or can be evaluated usingart-recognized animal models. In an embodiment, described herein is amethod of treating inflammatory disorders ranging from autoimmunediseases (e.g., rheumatoid arthritis, multiple sclerosis) to allergicinflammatory disorders, such as asthma and COPD using a compounddescribed herein.

For example, inhibitors of PI3Kδ and/or γ have been shown to haveanti-inflammatory activity in several autoimmune animal models forrheumatoid arthritis (Williams, O. et al. (2010) Chem Biol,17(2):123-34; WO 2009/088986; WO2009/088880; WO 2011/008302). PI3Kδ isexpressed in the RA synovial tissue (especially in the synovial liningwhich contains fibroblast-like synoviocytes (FLS), and selective PI3Kdinhibitors have been shown to be effective in inhibiting synoviocytegrowth and survival (Bartok et al. (2010) Arthritis Rheum 62 Suppl10:362). Several PI3K δ and γ inhibitors have been shown to amelioratearthritic symptoms (e.g., swelling of joints, reduction of serum-inducedcollagen levels, reduction of joint pathology and/or inflammation), inart-recognized models for RA, such as collagen-induced arthritis andadjuvant induced arthritis (WO 2009/088986; WO2009/088880; WO2011/008302).

The role of PI3K-δ has also been shown in models of T-cell dependentresponse, including the DTH model. In the murine experimental autoimmuneencephalomyelitis (EAE) model of multiple sclerosis, the PI3K-g/d-doublemutant mice are resistant. PI3K-δ inhibitors have also been shown toblock EAE disease induction and development of TH-17 cells both in vitroand in vivo (Haylock-Jacobs, S. et al. (2011) J. Autoimmunity36(3-4):278-87).

Systemic lupus erythematosus (SLE) is a complex disease that atdifferent stages requires memory T-cells, B-cell polyclonal expansionand differentiation into plasma cells, and the innate immune reasponseto endogenous damage associated molecular pattern molecules (DAMPS), andthe inflammatory responses to immune complexes through the complementsystem as well as the F_(C) receptors. The role of PI3K-δ and PI3K-γtogether in these pathways and cell types suggest that blockade with aninhibitor would be effective in these diseases. A role for PI3K in lupusis also predicted by two genetic models of lupus. The deletion ofphosphatase and tensin homolog (PTEN) leads to a lupus-like phenotype,as does a transgenic activation of Class1A PI3Ks, which includes PI3K-δ.The deletion of PI3K-γ in the transgenically activated class 1A lupusmodel is protective, and treatment with a PI3K-γ selective inhibitor inthe murine MLR/lpr model of lupus improves symptoms (Barber, D F et al.(2006) J. Immunol. 176(1): 589-93).

In allergic disease, PI3K-δ has been shown by genetic models and byinhibitor treatment to be essential for mast-cell activation in apassive cutaneous anaphalaxis assay (Ali K et al. (2008) J Immunol.180(4):2538-44; Ali K, (2004) Nature 431(7011):1007-11). In a pulmonarymeasure of response to immune complexes (Arthus reaction) a PI3K-δknockout is resistant, showing a defect in macrophage activation and C5aproduction. Knockout studies and studies with inhibitors for both PI3K-δand PI3K-γ support a role for both of these enzymes in the ovalbumininduced allergic airway inflammation and hyper-responsiveness model (LeeK S et al. (2006) FASEB J. 20(3):455-65). Reductions of infiltration ofeosinophils, neutrophils, and lymphocytes as well as TH2 cytokines (IL4,IL5, and IL13) were seen with both PI3K-δ specific and dual PI3K-δ andPI3K-γ inhibitors in the Ova induced asthma model (Lee K S et al. (2006)J Allergy Clin Immunol 118(2):403-9).

PI3K-δ and PI3K-γ inhibition can be used in treating COPD. In the smokedmouse model of COPD, the PI3K-δ knockout does not develop smoke inducedglucocorticoid resistance, while wild-type and PI3K-γ knockout mice do.An inhaled formulation of dual PI3K-δ and PI3K-γ inhibitor blockedinflammation in a LPS or smoke COPD models as measured by neutrophiliaand glucocorticoid resistance (Doukas J, et al. (2009) J Pharmacol ExpTher. 328(3):758-65).

Class I PI3Ks, particularly PI3Kδ and PI3Kγ isoforms, are alsoassociated with cancers (reviewed, e.g., in Vogt, P K et al. (2010) CurrTop Microbiol Immunol. 347:79-104; Fresno Vara, J A et al. (2004) CancerTreat Rev. 30(2):193-204; Zhao, L and Vogt, P K. (2008) Oncogene27(41):5486-96). Inhibitors of PI3K, e.g., PI3Kδ and/or γ, have beenshown to have anti-cancer activity (e.g., Courtney, K D et al. (2010) JClin Oncol. 28(6):1075-1083); Markman, B et al. (2010) Ann Oncol.21(4):683-91; Kong, D and Yamori, T (2009) Curr Med Chem.16(22):2839-54; Jimeno, A et al. (2009) J Clin Oncol. 27:156s (suppl;abstr 3542); Flinn, I W et al. (2009) J Clin Oncol. 27:156s (suppl;abstr 3543); Shapiro, G et al. (2009) J Clin Oncol. 27:146s (suppl;abstr 3500); Wagner, A J et al. (2009) J Clin Oncol. 27:146s (suppl;abstr 3501); Vogt, P K et al. (2006) Virology 344(1):131-8; Ward, S etal. (2003) Chem Biol. 10(3):207-13; WO 2011/041399; US 2010/0029693; US2010/0305096; US 2010/0305084). In an embodiment, described herein is amethod of treating cancer.

Types of cancer that can be treated with an inhibitor of PI3K(particularly, PI3Kδ and/or γ) include, e.g., leukemia, chroniclymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia(e.g., Salmena, L et al. (2008) Cell 133:403-414; Chapuis, N et al.(2010) Clin Cancer Res. 16(22):5424-35; Khwaja, A (2010) Curr TopMicrobiol Immunol. 347:169-88); lymphoma, e.g., non-Hodgkin's lymphoma(e.g., Salmena, L et al. (2008) Cell 133:403-414); lung cancer, e.g.,non-small cell lung cancer, small cell lung cancer (e.g., Herrera, V Aet al. (2011) Anticancer Res. 31(3):849-54); melanoma (e.g., Haluska, Fet al. (2007) Semin Oncol. 34(6):546-54); prostate cancer (e.g., Sarker,D et al. (2009) Clin Cancer Res. 15(15):4799-805); glioblastoma (e.g.,Chen, J S et al. (2008) Mol Cancer Ther. 7:841-850); endometrial cancer(e.g., Bansal, N et al. (2009) Cancer Control. 16(1):8-13); pancreaticcancer (e.g., Furukawa, T (2008) J Gastroenterol. 43(12):905-11); renalcell carcinoma (e.g., Porta, C and Figlin, R A (2009) J Urol.182(6):2569-77); colorectal cancer (e.g., Saif, M W and Chu, E (2010)Cancer J. 16(3):196-201); breast cancer (e.g., Torbett, N E et al.(2008) Biochem J. 415:97-100); thyroid cancer (e.g., Brzezianska, E andPastuszak-Lewandoska, D (2011) Front Biosci. 16:422-39); and ovariancancer (e.g., Mazzoletti, M and Broggini, M (2010) Curr Med Chem.17(36):4433-47).

Numerous publications support a role of PI3K-δ and PI3K-γ in treatinghematological cancers. PI3K-δ and PI3K-γ are highly expressed in theheme compartment, and some solid tumors, including prostate, breast andglioblastomas (Chen J. S. et al. (2008) Mol Cancer Ther. 7(4):841-50;Ikeda H. et al. (2010) Blood 116(9):1460-8). In hematological cancersincluding acute myeloid leukemia (AML), multiple myeloma (MM), andchronic lymphocytic leukemia (CLL), overexpression and constitutiveactivation of PI3K-δ supports the model that PI3K-δ inhibition would betherapeutic Billottet C, et al. (2006) Oncogene 25(50):6648-59;Billottet C, et al. (2009) Cancer Res. 69(3):1027-36; Meadows, S A,52^(nd) Annual ASH Meeting and Exposition; 2010 Dec. 4-7; Orlando, Fla.;Ikeda H, et al. (2010) Blood 116(9):1460-8; Herman S E et al. (2010)Blood 116(12):2078-88; Herman S E et al. (2011). Blood 117(16):4323-7.In an embodiment, described herein is a method of treating hematologicalcancers including, but not limited to acute myeloid leukemia (AML),multiple myeloma (MM), and chronic lymphocytic leukemia (CLL).

A PI3K-δ inhibitor (CAL-101) has been evaluated in a phase 1 trial inpatients with haematological malignancies, and showed activity in CLL inpatients with poor prognostic characteristics. In CLL, inhibition ofPI3K-δ not only affects tumor cells directly, but it also affects theability of the tumor cells to interact with their microenvironment. Thismicroenvironment includes contact with and factors from stromal cells,T-cells, nurse like cells, as well as other tumor cells. CAL-101suppresses the expression of stromal and T-cell derived factorsincluding CCL3, CCL4, and CXCL13, as well as the CLL tumor cells'ability to respond to these factors. CAL-101 treatment in CLL patientsinduces rapid lymph node reduction and redistribution of lymphocytesinto the circulation, and affects tonic survival signals through theBCR, leading to reduced cell viability, and an increase in apoptosis.Single agent CAL-101 treatment was also active in mantle cell lymphomaand refractory non Hodgkin's lymphoma (Furman, R R, et al. 52^(nd)Annual ASH Meeting and Exposition; 2010 Dec. 4-7; Orlando, Fla.;Hoellenriegel, J, et al. 52^(nd) Annual ASH Meeting and Exposition; 2010Dec. 4-7; Orlando, Fla.; Webb, H K, et al. 52^(nd) Annual ASH Meetingand Exposition; 2010 Dec. 4-7; Orlando, Fla.; Meadows, et al. 52^(nd)Annual ASH Meeting and Exposition; 2010 Dec. 4-7; Orlando, Fla.; Kahl,B, et al. 52^(nd) Annual ASH Meeting and Exposition; 2010 Dec. 4-7;Orlando, Fla.; Lannutti B J, et al. (2011) Blood 117(2):591-4).

PI3K-δ inhibitors have shown activity against PI3K-δ positive gliomas invitro (Kashishian A, et al. Poster presented at: The AmericanAssociation of Cancer Research 102^(nd) Annual Meeting; 2011 Apr. 2-6;Orlando, Fla.). PI3K-β is the PI3K isoform that is most commonlyactivated in tumors where the PTEN tumor suppressor is mutated (Ward S,et al. (2003) Chem Biol. 10(3):207-13). In this subset of tumors,treatment with the PI3K-δ inhibitor either alone or in combination witha cytotoxic agent can be effective.

Another mechanism for PI3K-δ inhibitors to have an affect in solidtumors involves the tumor cells' interaction with theirmicro-environment. PI3K-δ, PI3K-γ, and PI3K-β are expressed in theimmune cells that infiltrate tumors, including tumor infiltratinglymphocytes, macrophages, and neutrophils. PI3K-δ inhibitors can modifythe function of these tumor-associated immune cells and how they respondto signals from the stroma, the tumor, and each other, and in this wayaffect tumor cells and metastasis (Hoellenriegel, J, et al. 52^(nd)Annual ASH Meeting and Exposition; 2010 Dec. 4-7; Orlando, Fla.).

PI3K-δ is also expressed in endothelial cells. It has been shown thattumors in mice treated with PI3K-δ selective inhibitors are killed morereadily by radiation therapy. In this same study, capillary networkformation is impaired by the PI3K inhibitor, and it is postulated thatthis defect contributes to the greater killing with radiation. PI3K-δinhibitors can affect the way in which tumors interact with theirmicroenviroment, including stromal cells, immune cells, and endothelialcells and be therapeutic either on its own or in conjunction withanother therapy (Meadows, S A, et al. Paper presented at: 52^(nd) AnnualASH Meeting and Exposition; 2010 Dec. 4-7; Orlando, Fla.; Geng L, et al.(2004) Cancer Res. 64(14):4893-9).

In some embodiments, provided herein are methods of using the compoundsor pharmaceutical compositions to treat disease conditions, includingbut not limited to diseases associated with malfunctioning of one ormore types of PI3 kinase. A detailed description of conditions anddisorders mediated by p110δ kinase activity is set forth in Sadu et al.,WO 01/81346, which is incorporated herein by reference in its entiretyfor all purposes.

The treatment methods provided herein comprise administering to thesubject a therapeutically effective amount of a compound as disclosedherein.

In some embodiments, the disclosure relates to a method of treating ahyperproliferative disorder in a subject that comprises administering tosaid subject a therapeutically effective amount of a compound asdisclosed herein, or a pharmaceutically acceptable form, salt, ester,prodrug or derivative thereof. In some embodiments, said method relatesto the treatment of cancer such as acute myeloid leukemia, thymus,brain, lung, squamous cell, skin, eye, retinoblastoma, intraocularmelanoma, oral cavity and oropharyngeal, bladder, gastric, stomach,pancreatic, bladder, breast, cervical, head, neck, renal, kidney, liver,ovarian, prostate, colorectal, esophageal, testicular, gynecological,thyroid, CNS, PNS, AIDS-related (e.g., Lymphoma and Kaposi's Sarcoma) orviral-induced cancer. In some embodiments, said method relates to thetreatment of a non-cancerous hyperproliferative disorder such as benignhyperplasia of the skin (e.g., psoriasis), restenosis, or prostate(e.g., benign prostatic hypertrophy (BPH)).

In one embodiment, provided herein is a method of treating aninflammation disorder, including autoimmune diseases in a subject. Themethod comprises administering to said subject a therapeuticallyeffective amount of a compound as disclosed herein, or apharmaceutically acceptable form, salt, ester, prodrug or derivativethereof. Examples of autoimmune diseases includes but is not limited toacute disseminated encephalomyelitis (ADEM), Addison's disease,antiphospholipid antibody syndrome (APS), aplastic anemia, autoimmunehepatitis, coeliac disease, Crohn's disease, Diabetes mellitus (type 1),Goodpasture's syndrome, Graves' disease, Guillain-Barré syndrome (GBS),Hashimoto's disease, lupus erythematosus, multiple sclerosis, myastheniagravis, opsoclonus myoclonus syndrome (OMS), optic neuritis, Ord'sthyroiditis, oemphigus, polyarthritis, primary biliary cirrhosis,psoriasis, rheumatoid arthritis, Reiter's syndrome, Takayasu'sarteritis, temporal arteritis (also known as “giant cell arteritis”),warm autoimmune hemolytic anemia, Wegener's granulomatosis, alopeciauniversalis, Chagas disease, chronic fatigue syndrome, dysautonomia,endometriosis, hidradenitis suppurativa, interstitial cystitis,neuromyotonia, sarcoidosis, scleroderma, ulcerative colitis, vitiligo,and vulvodynia. Other disorders include bone-resorption disorders andthrombosis.

In some embodiments, provided herein are methods for treating disordersor conditions in which the δ isoform of PI3K is implicated to a greaterextent than other PI3K isoforms such as PI3K α and/or β. Selectiveinhibition of PI3K-δ and/or PI3K-γ can provide advantages over usingless selective compounds which inhibit PI3K α and/or β, such as animproved side effects profile or lessened reduction in the ability toreduce a bacterial, viral, and/or fungal infection.

In certain embodiments, a method of treating inflammatory or autoimmunediseases is provided comprising administering to a subject (e.g., amammal) a therapeutically effective amount of one or more compounds asdisclosed herein that selectively inhibit PI3K-δ and/or PI3K-γ ascompared to all other type I PI3 kinases. Such selective inhibition ofPI3K-δ and/or PI3K-γ can be advantageous for treating any of thediseases or conditions described herein. For example, selectiveinhibition of PI3K-δ can inhibit inflammatory responses associated withinflammatory diseases, autoimmune disease, or diseases related to anundesirable immune response including but not limited to asthma,emphysema, allergy, dermatitis, rheumatoid arthritis, psoriasis, lupuserythematosus, or graft versus host disease. Selective inhibition ofPI3K-δ can further provide for a reduction in the inflammatory orundesirable immune response without a concomittant reduction in theability to reduce a bacterial, viral, and/or fungal infection. Selectiveinhibition of both PI3K-δ and PI3K-γ can be advantageous for inhibitingthe inflammatory response in the subject to a greater degree than thatwould be provided for by inhibitors that selectively inhibit PI3K-δ orPI3K-γ alone. In one aspect, one or more of the subject methods areeffective in reducing antigen specific antibody production in vivo byabout 2-fold, 3-fold, 4-fold, 5-fold, 7.5-fold, 10-fold, 25-fold,50-fold, 100-fold, 250-fold, 500-fold, 750-fold, or about 1000-fold ormore. In another aspect, one or more of the subject methods areeffective in reducing antigen specific IgG3 and/or IgGM production invivo by about 2-fold, 3-fold, 4-fold, 5-fold, 7.5-fold, 10-fold,25-fold, 50-fold, 100-fold, 250-fold, 500-fold, 750-fold, or about1000-fold or more.

In one aspect, one of more of the subject methods are effective inameliorating symptoms associated with rhuematoid arthritis including butnot limited to a reduction in the swelling of joints, a reduction inserum anti-collagen levels, and/or a reduction in joint pathology suchas bone resorption, cartilage damage, pannus, and/or inflammation. Inanother aspect, the subject methods are effective in reducing ankleinflammation by at least about 2%, 5%, 10%, 15%, 20%, 25%, 30%, 50%,60%, or about 75% to 90%. In another aspect, the subject methods areeffective in reducing knee inflammation by at least about 2%, 5%, 10%,15%, 20%, 25%, 30%, 50%, 60%, or about 75% to 90% or more. In stillanother aspect, the subject methods are effective in reducing serumanti-type II collagen levels by at least about 10%, 12%, 15%, 20%, 24%,25%, 30%, 35%, 50%, 60%, 75%, 80%, 86%, 87%, or about 90% or more. Inanother aspect, the subject methods are effective in reducing anklehistopathology scores by about 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%,60%, 75%, 80%, 90% or more. In still another aspect, the subject methodsare effective in reducing knee histopathology scores by about 5%, 10%,15%, 20%, 25%, 30%, 40%, 50%, 60%, 75%, 80%, 90% or more.

In other embodiments, provided herein are methods of using the compoundsor pharmaceutical compositions to treat respiratory diseases includingbut not limited to diseases affecting the lobes of lung, pleural cavity,bronchial tubes, trachea, upper respiratory tract, or the nerves andmuscle for breathing. For example, methods are provided to treatobstructive pulmonary disease. Chronic obstructive pulmonary disease(COPD) is an umbrella term for a group of respiratory tract diseasesthat are characterized by airflow obstruction or limitation. Conditionsincluded in this umbrella term include, but are not limited to: chronicbronchitis, emphysema, and bronchiectasis.

In another embodiment, the compounds described herein are used for thetreatment of asthma. Also, the compounds or pharmaceutical compositionsdescribed herein can be used for the treatment of endotoxemia andsepsis. In one embodiment, the compounds or pharmaceutical compositionsdescribed herein are used to for the treatment of rheumatoid arthritis(RA). In yet another embodiment, the compounds or pharmaceuticalcompositions described herein is used for the treatment of contact oratopic dermatitis. Contact dermatitis includes irritant dermatitis,phototoxic dermatitis, allergic dermatitis, photoallergic dermatitis,contact urticaria, systemic contact-type dermatitis and the like.Irritant dermatitis can occur when too much of a substance is used onthe skin of when the skin is sensitive to certain substance. Atopicdermatitis, sometimes called eczema, is a kind of dermatitis, an atopicskin disease.

In some embodiments, the disclosure provides a method of treatingdiseases related to vasculogenesis or angiogenesis in a subject thatcomprises administering to said subject a therapeutically effectiveamount of a compound as disclosed herein, or a pharmaceuticallyacceptable form, salt, ester, prodrug, or derivative thereof. In someembodiments, said method is for treating a disease selected from tumorangiogenesis, chronic inflammatory disease such as rheumatoid arthritis,atherosclerosis, inflammatory bowel disease, skin diseases such aspsoriasis, eczema, and scleroderma, diabetes, diabetic retinopathy,retinopathy of prematurity, age-related macular degeneration,hemangioma, glioma, melanoma, Kaposi's sarcoma and ovarian, breast,lung, pancreatic, prostate, colon and epidermoid cancer.

Patients that can be treated with compounds as disclosed herein, orpharmaceutically acceptable form, salt, ester, prodrug or derivative ofsaid compounds, according to the methods as disclosed herein include,for example, but not limited to, patients that have been diagnosed ashaving psoriasis; restenosis; atherosclerosis; BPH; breast cancer suchas a ductal carcinoma in duct tissue in a mammary gland, medullarycarcinomas, colloid carcinomas, tubular carcinomas, and inflammatorybreast cancer; ovarian cancer, including epithelial ovarian tumors suchas adenocarcinoma in the ovary and an adenocarcinoma that has migratedfrom the ovary into the abdominal cavity; uterine cancer; cervicalcancer such as adenocarcinoma in the cervix epithelial includingsquamous cell carcinoma and adenocarcinomas; prostate cancer, such as aprostate cancer selected from the following: an adenocarcinoma or anadenocarinoma that has migrated to the bone; pancreatic cancer such asepitheliod carcinoma in the pancreatic duct tissue and an adenocarcinomain a pancreatic duct; bladder cancer such as a transitional cellcarcinoma in urinary bladder, urothelial carcinomas (transitional cellcarcinomas), tumors in the urothelial cells that line the bladder,squamous cell carcinomas, adenocarcinomas, and small cell cancers;leukemia such as acute myeloid leukemia (AML), acute lymphocyticleukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, hairycell leukemia, myelodysplasia, myeloproliferative disorders, acutemyelogenous leukemia (AML), chronic myelogenous leukemia (CML),mastocytosis, chronic lymphocytic leukemia (CLL), multiple myeloma (MM),and myelodysplastic syndrome (MDS); bone cancer; lung cancer such asnon-small cell lung cancer (NSCLC), which is divided into squamous cellcarcinomas, adenocarcinomas, and large cell undifferentiated carcinomas,and small cell lung cancer; skin cancer such as basal cell carcinoma,melanoma, squamous cell carcinoma and actinic keratosis, which is a skincondition that sometimes develops into squamous cell carcinoma; eyeretinoblastoma; cutaneous or intraocular (eye) melanoma; primary livercancer (cancer that begins in the liver); kidney cancer; thyroid cancersuch as papillary, follicular, medullary and anaplastic; AIDS-relatedlymphoma such as diffuse large B-cell lymphoma, B-cell immunoblasticlymphoma and small non-cleaved cell lymphoma; Kaposi's Sarcoma;viral-induced cancers including hepatitis B virus (HBV), hepatitis Cvirus (HCV), and hepatocellular carcinoma; human lymphotropic virus-type1 (HTLV-1) and adult T-cell leukemia/lymphoma; and human papilloma virus(HPV) and cervical cancer; central nervous system cancers (CNS) such asprimary brain tumor, which includes gliomas (astrocytoma, anaplasticastrocytoma, or glioblastoma multiforme), Oligodendroglioma, Ependymoma,Meningioma, Lymphoma, Schwannoma, and Medulloblastoma; peripheralnervous system (PNS) cancers such as acoustic neuromas and malignantperipheral nerve sheath tumor (MPNST) including neurofibromas andschwannomas, malignant fibrous cytoma, malignant fibrous histiocytoma,malignant meningioma, malignant mesothelioma, and malignant mixedMüllerian tumor; oral cavity and oropharyngeal cancer such as,hypopharyngeal cancer, laryngeal cancer, nasopharyngeal cancer, andoropharyngeal cancer; stomach cancer such as lymphomas, gastric stromaltumors, and carcinoid tumors; testicular cancer such as germ cell tumors(GCTs), which include seminomas and nonseminomas, and gonadal stromaltumors, which include Leydig cell tumors and Sertoli cell tumors; thymuscancer such as to thymomas, thymic carcinomas, Hodgkin disease,non-Hodgkin lymphomas carcinoids or carcinoid tumors; rectal cancer; andcolon cancer.

In some embodiments, the disclosure relates to a method of treatingdiabetes in a subject that comprises administering to said subject atherapeutically effective amount of a compound as disclosed herein, or apharmaceutically acceptable form, salt, ester, prodrug or derivativethereof.

In addition, the compounds described herein can be used to treat acne.

In addition, the compounds described herein can be used for thetreatment of arteriosclerosis, including atherosclerosis.Arteriosclerosis is a general term describing any hardening of medium orlarge arteries. Atherosclerosis is a hardening of an artery specificallydue to an atheromatous plaque.

Further, the compounds described herein can be used for the treatment ofglomerulonephritis. Glomerulonephritis is a primary or secondaryautoimmune renal disease characterized by inflammation of the glomeruli.It can be asymptomatic, or present with hematuria and/or proteinuria.There are many recognized types, divided in acute, subacute or chronicglomerulonephritis. Causes are infectious (bacterial, viral or parasiticpathogens), autoimmune or paraneoplastic.

Additionally, the compounds described herein can be used for thetreatment of bursitis, lupus, acute disseminated encephalomyelitis(ADEM), Addison's disease, antiphospholipid antibody syndrome (APS),aplastic anemia, autoimmune hepatitis, coeliac disease, crohn's disease,diabetes mellitus (type 1), goodpasture's syndrome, graves' disease,guillain-barré syndrome (GBS), hashimoto's disease, inflammatory boweldisease, lupus erythematosus, myasthenia gravis, opsoclonus myoclonussyndrome (OMS), optic neuritis, ord's thyroiditis, ostheoarthritis,uveoretinitis, pemphigus, polyarthritis, primary biliary cirrhosis,reiter's syndrome, takayasu's arteritis, temporal arteritis, warmautoimmune hemolytic anemia, wegener's granulomatosis, alopeciauniversalis, chagas' disease, chronic fatigue syndrome, dysautonomia,endometriosis, hidradenitis suppurativa, interstitial cystitis,neuromyotonia, sarcoidosis, scleroderma, ulcerative colitis, vitiligo,vulvodynia, appendicitis, arteritis, arthritis, blepharitis,bronchiolitis, bronchitis, cervicitis, cholangitis, cholecystitis,chorioamnionitis, colitis, conjunctivitis, cystitis, dacryoadenitis,dermatomyositis, endocarditis, endometritis, enteritis, enterocolitis,epicondylitis, epididymitis, fasciitis, fibrositis, gastritis,gastroenteritis, gingivitis, hepatitis, hidradenitis, ileitis, iritis,laryngitis, mastitis, meningitis, myelitis, myocarditis, myositis,nephritis, omphalitis, oophoritis, orchitis, osteitis, otitis,pancreatitis, parotitis, pericarditis, peritonitis, pharyngitis,pleuritis, phlebitis, pneumonitis, proctitis, prostatitis,pyelonephritis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis,tendonitis, tonsillitis, uveitis, vaginitis, vasculitis, or vulvitis.

In some embodiments, provided herein is a method of treating acardiovascular disease in a subject that comprises administering to saidsubject a therapeutically effective amount of a compound as disclosedherein, or a pharmaceutically acceptable form, salt, ester, prodrug orderivative thereof. Examples of cardiovascular conditions include, butare not limited to, atherosclerosis, restenosis, vascular occlusion andcarotid obstructive disease.

In another aspect, provided herein are methods of disrupting thefunction of a leukocyte or disrupting a function of an osteoclast. Themethod includes contacting the leukocyte or the osteoclast with afunction disrupting amount of a compound as disclosed herein.

In another aspect, methods are provided for treating ophthalmic diseaseby administering one or more of the subject compounds or pharmaceuticalcompositions to the eye of a subject.

Methods are further provided for administering the compounds providedherein include via eye drop, intraocular injection, intravitrealinjection, topically, or through the use of a drug eluting device,microcapsule, implant, or microfluidic device. In some cases, thecompounds as disclosed herein are administered with a carrier orexcipient that increases the intraocular penetrance of the compound suchas an oil and water emulsion with colloid particles having an oily coresurrounded by an interfacial film. It is contemplated that all localroutes to the eye can be used including topical, subconjunctival,periocular, retrobulbar, subtenon, intracameral, intravitreal,intraocular, subretinal, juxtascleral and suprachoroidal administration.Systemic or parenteral administration can be feasible including but notlimited to intravenous, subcutaneous, and oral delivery. An exemplarymethod of administration will be intravitreal or subtenon injection ofsolutions or suspensions, or intravitreal or subtenon placement ofbioerodible or non-bioerodible devices, or by topical ocularadministration of solutions or suspensions, or posterior juxtascleraladministration of a gel or cream formulation.

In some cases, the colloid particles include at least one cationic agentand at least one non-ionic sufactant such as a poloxamer, tyloxapol, apolysorbate, a polyoxyethylene castor oil derivative, a sorbitan ester,or a polyoxyl stearate. In some cases, the cationic agent is analkylamine, a tertiary alkyl amine, a quarternary ammonium compound, acationic lipid, an amino alcohol, a biguanidine salt, a cationiccompound or a mixture thereof. In some cases, the cationic agent is abiguanidine salt such as chlorhexidine, polyaminopropyl biguanidine,phenformin, alkylbiguanidine, or a mixture thereof. In some cases, thequaternary ammonium compound is a benzalkonium halide, lauralkoniumhalide, cetrimide, hexadecyltrimethylammonium halide,tetradecyltrimethylammonium halide, dodecyltrimethylammonium halide,cetrimonium halide, benzethonium halide, behenalkonium halide,cetalkonium halide, cetethyldimonium halide, cetylpyridinium halide,benzododecinium halide, chlorallyl methenamine halide, rnyristylalkoniumhalide, stearalkonium halide or a mixture of two or more thereof. Insome cases, cationic agent is a benzalkonium chloride, lauralkoniumchloride, benzododecinium bromide, benzethenium chloride,hexadecyltrimethylammonium bromide, tetradecyltrimethylammonium bromide,dodecyltrimethylammonium bromide or a mixture of two or more thereof. Insome cases, the oil phase is mineral oil and light mineral oil, mediumchain triglycerides (MCT), coconut oil; hydrogenated oils comprisinghydrogenated cottonseed oil, hydrogenated palm oil, hydrogenate castoroil or hydrogenated soybean oil; polyoxyethylene hydrogenated castor oilderivatives comprising polyoxyl-40 hydrogenated castor oil, polyoxyl-60hydrogenated castor oil or polyoxyl-100 hydrogenated castor oil.

In some embodiments, provided herein are methods of modulating a PI3Kkinase activity by contacting the kinase with an effective amount of acompound as disclosed herein. Modulation can be inhibiting or activatingkinase activity. In some embodiments, provided herein are methods ofinhibiting kinase activity by contacting the kinase with an effectiveamount of a compound as disclosed herein in solution. In someembodiments, provided herein are methods of inhibiting the kinaseactivity by contacting a cell, tissue, organ that express the kinase ofinterest. In some embodiments, provided herein are methods of inhibitingkinase activity in a subject by administering into the subject aneffective amount of a compound as disclosed herein. In some embodiments,the percentage of inhibiting exceeds about 25%, 30%, 40%, 50%, 60%, 70%,80%, or 90%.

In some embodiments, the kinase is a lipid kinase or a protein kinase.In some embodiments, the kinase is selected from a PI3 kinase includingdifferent isoforms such as PI3 kinase α, PI3 kinase β, PI3 kinase γ, PI3kinase δ; DNA-PK; mTor; Abl, VEGFR, Ephrin receptor B4 (EphB4); TEKreceptor tyrosine kinase (TIE2); FMS-related tyrosine kinase 3 (FLT-3);Platelet derived growth factor receptor (PDGFR); RET; ATM; ATR; hSmg-1;Hck; Src; Epidermal growth factor receptor (EGFR); KIT; Inulsin Receptor(IR) and IGFR.

In some embodiments, disclosed herein are methods of modulating PI3kinase activity by contacting a PI3 kinase with an amount of a compoundas disclosed herein sufficient to modulate the activity of the PI3kinase. Modulate can be inhibiting or activating PI3 kinase activity. Insome embodiments, provided herein are methods of inhibiting PI3 kinaseactivity by contacting a PI3 kinase with an amount of a compound asdisclosed herein sufficient to inhibit the activity of the PI3 kinase.In some embodiments, provided herein are methods of inhibiting PI3kinase activity. Such inhibition can take place in solution, in a cellexpressing one or more PI3 kinases, in a tissue comprising a cellexpressing one or more PI3 kinases, or in an organism expressing one ormore PI3 kinases. In some embodiments, provided herein are methods ofinhibiting PI3 kinase activity in a subject (including mammals such ashumans) by contacting said subject with an amount of a compound asdisclosed herein sufficient to inhibit the activity of the PI3 kinase insaid subject.

In some embodiments, provided herein are methods for combinationtherapies in which an agent known to modulate other pathways, or othercomponents of the same pathway, or even overlapping sets of targetenzymes are used in combination with a compound as disclosed herein, ora pharmaceutically acceptable form, salt, ester, prodrug or derivativethereof. In one aspect, such therapy includes, but is not limited to,the combination of the subject compound with chemotherapeutic agents,therapeutic antibodies, and radiation treatment, to provide asynergistic or additive therapeutic effect.

In one aspect, the compounds or pharmaceutical compositions as disclosedherein can present synergistic or additive efficacy when administered incombination with agents that inhibit IgE production or activity. Suchcombination can reduce the undesired effect of high level of IgEassociated with the use of one or more PI3Kδ inhibitors, if such effectoccurs. This can be particularly useful in treatment of autoimmune andinflammatory disorders (AIID) such as rheumatoid arthritis.Additionally, the administration of PI3Kδ or PI3Kδ/γ inhibitors asdisclosed herein in combination with inhibitors of mTOR can also exhibitsynergy through enhanced inhibition of the PI3K pathway.

In a separate but related aspect, provided herein is a combinationtreatment of a disease associated with PI3Kδ comprising administering toa PI3Kδ inhibitor and an agent that inhibits IgE production or activity.Other exemplary PI3Kδ inhibitors are applicable for this combination andthey are described, e.g., U.S. Pat. No. 6,800,620. Such combinationtreatment is particularly useful for treating autoimmune andinflammatory diseases (AIID) including but not limited to rheumatoidarthritis.

Agents that inhibit IgE production are known in the art and theyinclude, but are not limited to, one or more of TEI-9874,2-(4-(6-cyclohexyloxy-2-naphtyloxy)phenylacetamide)benzoic acid,rapamycin, rapamycin analogs (i.e., rapalogs), TORC1 inhibitors, TORC2inhibitors, and any other compounds that inhibit mTORC1 and mTORC2.Agents that inhibit IgE activity include, for example, anti-IgEantibodies such as for example Omalizumab and TNX-901.

For treatment of autoimmune diseases, the subject compounds orpharmaceutical compositions can be used in combination with commonlyprescribed drugs including but not limited to Enbrel®, Remicade®,Humira®, Avonex®, and Rebif®. For treatment of respiratory diseaseses,the subject compounds or pharmaceutical compositions can be administeredin combination with commonly prescribed drugs including but not limitedto Xolair®, Advair®, Singulair®, and Spiriva®.

The compounds as disclosed herein can be formulated or administered inconjunction with other agents that act to relieve the symptoms ofinflammatory conditions such as encephalomyelitis, asthma, and the otherdiseases described herein. These agents include non-steroidalanti-inflammatory drugs (NSAIDs), e.g., acetylsalicylic acid; ibuprofen;naproxen; indomethacin; nabumetone; tolmetin; etc. Corticosteroids areused to reduce inflammation and suppress activity of the immune system.An exemplary drug of this type is Prednisone. Chloroquine (Aralen) orhydroxychloroquine (Plaquenil) can also be used in some individuals withlupus. They can be prescribed for skin and joint symptoms of lupus.Azathioprine (Imuran) and cyclophosphamide (Cytoxan) suppressinflammation and tend to suppress the immune system. Other agents, e.g.,methotrexate and cyclosporin are used to control the symptoms of lupus.Anticoagulants are employed to prevent blood from clotting rapidly. Theyrange from aspirin at very low dose which prevents platelets fromsticking, to heparin/coumadin.

In another aspect, provided herein is a pharmaceutical composition forinhibiting abnormal cell growth in a subject which comprises an amountof a compound as disclosed herein, or a pharmaceutically acceptableform, salt, ester, prodrug or derivative thereof, in combination with anamount of an anti-cancer agent (e.g., a chemotherapeutic agent). Manychemotherapeutics are presently known in the art and can be used incombination with the compounds as disclosed herein.

In some embodiments, the chemotherapeutic is selected from mitoticinhibitors, alkylating agents, anti-metabolites, intercalatingantibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes,topoisomerase inhibitors, biological response modifiers, anti-hormones,angiogenesis inhibitors, and anti-androgens. Non-limiting examples arechemotherapeutic agents, cytotoxic agents, and non-peptide smallmolecules such as Gleevec® (Imatinib Mesylate), Velcade® (bortezomib),Casodex (bicalutamide), Iressa®, and Adriamycin as well as a host ofchemotherapeutic agents. Non-limiting examples of chemotherapeuticagents include alkylating agents such as thiotepa and cyclosphosphamide(CYTOXAN™); alkyl sulfonates such as busulfan, improsulfan andpiposulfan; aziridines such as benzodopa, carboquone, meturedopa, anduredopa; ethylenimines and methylamelamines including altretamine,triethylenemelamine, trietylenephosphoramide,triethylenethiophosphaoramide and trimethylolomelamine; nitrogenmustards such as chlorambucil, chlornaphazine, cholophosphamide,estramustine, ifosfamide, mechlorethamine, mechlorethamine oxidehydrochloride, melphalan, novembichin, phenesterine, prednimustine,trofosfamide, uracil mustard; nitrosureas such as carmustine,chlorozotocin, fotemustine, lomustine, nimustine, ranimustine;antibiotics such as aclacinomysins, actinomycin, authramycin, azaserine,bleomycins, cactinomycin, calicheamicin, carabicin, caminomycin,carzinophilin, Casodex™, chromomycins, dactinomycin, daunorubicin,detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin, epirubicin,esorubicin, idarubicin, marcellomycin, mitomycins, mycophenolic acid,nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin,quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin,ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexateand 5-fluorouracil (5-FU); folic acid analogues such as denopterin,methotrexate, pteropterin, trimetrexate; purine analogs such asfludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidineanalogs such as ancitabine, azacitidine, 6-azauridine, carmofur,cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine,androgens such as calusterone, dromostanolone propionate, epitiostanol,mepitiostane, testolactone; anti-adrenals such as aminoglutethimide,mitotane, trilostane; folic acid replenisher such as frolinic acid;aceglatone; aldophosphamide glycoside; aminolevulinic acid; amsacrine;bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;diaziquone; elfomithine; elliptinium acetate; etoglucid; galliumnitrate; hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone;mopidamol; nitracrine; pentostatin; phenamet; pirarubicin; podophyllinicacid; 2-ethylhydrazide; procarbazine; PSK.R™; razoxane; sizofuran;spirogermanium; tenuazonic acid; triaziquone;2,2′,2″-trichlorotriethylamine; urethan; vindesine; dacarbazine;mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxanes, e.g.,paclitaxel (TAXOL™, Bristol-Myers Squibb Oncology, Princeton, N.J.) anddocetaxel (TAXOTERE™, Rhone-Poulenc Rorer, Antony, France) and ABRAXANE®(paclitaxel protein-bound particles); retinoic acid; esperamicins;capecitabine; and pharmaceutically acceptable forms, salts, acids orderivatives of any of the above. Also included as suitablechemotherapeutic cell conditioners are anti-hormonal agents that act toregulate or inhibit hormone action on tumors such as anti-estrogensincluding for example tamoxifen (Nolvadex™), raloxifene, aromataseinhibiting 4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene,LY 117018, onapristone, and toremifene (Fareston); and anti-androgenssuch as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin;chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate;platinum analogs such as cisplatin and carboplatin; vinblastine;platinum; etoposide (VP-16); ifosfamide; mitomycin C; mitoxantrone;vincristine; vinorelbine; navelbine; novantrone; teniposide; daunomycin;aminopterin; xeloda; ibandronate; camptothecin-11 (CPT-11);topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO). Wheredesired, the compounds or pharmaceutical composition as disclosed hereincan be used in combination with commonly prescribed anti-cancer drugssuch as Herceptin®, Avastin®, Erbitux®, Rituxan®, Taxol®, Arimidex®,Taxotere®, ABVD, AVICINE, Abagovomab, Acridine carboxamide,Adecatumumab, 17-N-Allylamino-17-demethoxygeldanamycin, Alpharadin,Alvocidib, 3-Aminopyridine-2-carboxaldehyde thiosemicarbazone,Amonafide, Anthracenedione, Anti-CD22 immunotoxins, Antineoplastic,Antitumorigenic herbs, Apaziquone, Atiprimod, Azathioprine, Belotecan,Bendamustine, BIBW 2992, Biricodar, Brostallicin, Bryostatin, Buthioninesulfoximine, CBV (chemotherapy), Calyculin, cell-cycle nonspecificantineoplastic agents, Dichloroacetic acid, Discodermolide,Elsamitrucin, Enocitabine, Epothilone, Eribulin, Everolimus, Exatecan,Exisulind, Ferruginol, Forodesine, Fosfestrol, ICE chemotherapy regimen,IT-101, Imexon, Imiquimod, Indolocarbazole, Irofulven, Laniquidar,Larotaxel, Lenalidomide, Lucanthone, Lurtotecan, Mafosfamide,Mitozolomide, Nafoxidine, Nedaplatin, Olaparib, Ortataxel, PAC-1,Pawpaw, Pixantrone, Proteasome inhibitor, Rebeccamycin, Resiquimod,Rubitecan, SN-38, Salinosporamide A, Sapacitabine, Stanford V,Swainsonine, Talaporfin, Tariquidar, Tegafur-uracil, Temodar, Tesetaxel,Triplatin tetranitrate, Tris(2-chloroethyl)amine, Troxacitabine,Uramustine, Vadimezan, Vinflunine, ZD6126, and Zosuquidar.

In some embodiments, the chemotherapeutic is selected from hedgehoginhibitors including, but not limited to IPI-926 (See U.S. Pat. No.7,812,164). Other suitable hedgehog inhibitors include, for example,those described and disclosed in U.S. Pat. No. 7,230,004, U.S. PatentApplication Publication No. 2008/0293754, U.S. Patent ApplicationPublication No. 2008/0287420, and U.S. Patent Application PublicationNo. 2008/0293755, the entire disclosures of which are incorporated byreference herein. Examples of other suitable hedgehog inhibitors includethose described in U.S. Patent Application Publication Nos. US2002/0006931, US 2007/0021493 and US 2007/0060546, and InternationalApplication Publication Nos. WO 2001/19800, WO 2001/26644, WO2001/27135, WO 2001/49279, WO 2001/74344, WO 2003/011219, WO2003/088970, WO 2004/020599, WO 2005/013800, WO 2005/033288, WO2005/032343, WO 2005/042700, WO 2006/028958, WO 2006/050351, WO2006/078283, WO 2007/054623, WO 2007/059157, WO 2007/120827, WO2007/131201, WO 2008/070357, WO 2008/110611, WO 2008/112913, and WO2008/131354. Additional examples of hedgehog inhibitors include, but arenot limited to, GDC-0449 (also known as RG3616 or vismodegib) describedin, e.g., Von Hoff D. et al., N. Engl. J. Med. 2009; 361(12):1164-72;Robarge K. D. et al., Bioorg Med Chem Lett. 2009; 19(19):5576-81; Yauch,R. L. et al. (2009) Science 326: 572-574; Sciencexpress: 1-3(10.1126/science.1179386); Rudin, C. et al. (2009) New England J ofMedicine 361-366 (10.1056/nejma0902903); BMS-833923 (also known asXL139) described in, e.g., in Siu L. et al., J. Clin. Oncol. 2010;28:15s (suppl; abstr 2501); and National Institute of Health ClinicalTrial Identifier No. NCT006701891; LDE-225 described, e.g., in Pan S. etal., ACS Med. Chem. Lett., 2010; 1(3): 130-134; LEQ-506 described, e.g.,in National Institute of Health Clinical Trial Identifier No.NCT01106508; PF-04449913 described, e.g., in National Institute ofHealth Clinical Trial Identifier No. NCT00953758; Hedgehog pathwayantagonists disclosed in U.S. Patent Application Publication No.2010/0286114; SMOi2-17 described, e.g., U.S. Patent ApplicationPublication No. 2010/0093625; SANT-1 and SANT-2 described, e.g., inRominger C. M. et al., J. Pharmacol. Exp. Ther. 2009; 329(3):995-1005;1-piperazinyl-4-arylphthalazines or analogues thereof, described inLucas B. S. et al., Bioorg. Med. Chem. Lett. 2010; 20(12):3618-22.

In some embodiments, the chemotherapeutic is selected from HSP90inhibitors. The HSP90 inhibitor can be a geldanamycin derivative, e.g.,a benzoquinone or hygroquinone ansamycin HSP90 inhibitor (e.g., IPI-493and/or IPI-504). Non-limiting examples of HSP90 inhibitors includeIPI-493, IPI-504, 17-AAG (also known as tanespimycin or CNF-1010),BIIB-021 (CNF-2024), BIIB-028, AUY-922 (also known as VER-49009),SNX-5422, STA-9090, AT-13387, XL-888, MPC-3100, CU-0305, 17-DMAG,CNF-1010, Macbecin (e.g., Macbecin I, Macbecin II), CCT-018159,CCT-129397, PU-H71, or PF-04928473 (SNX-2112).

In some embodiments, the chemotherapeutic is selected from PI3Kinhibitors (e.g., including those PI3K inhibitors disclosed herein andthose PI3K inhibitors not disclosed herein). In some embodiment, thePI3K inhibitor is an inhibitor of delta and gamma isoforms of PI3K. Insome embodiments, the PI3K inhibitor is an inhibitor of alpha isoformsof PI3K. In other embodiments, the PI3K inhibitor is an inhibitor of oneor more alpha, beta, delta and gamma isoforms of PI3K. Exemplary PI3Kinhibitors that can be used in combination are described in, e.g., WO2010/036380; WO 2010/006086, WO 09/114,870, WO 05/113556. AdditionalPI3K inhibitors that can be used in combination with the pharmaceuticalcompositions, include but are not limited to, GSK 2126458, GDC-0980,GDC-0941, Sanofi XL147, XL756, XL147, PF-46915032, BKM 120, CAL-101, CAL263, SF1126, PX-886, and a dual PI3K inhibitor (e.g., Novartis BEZ235).In one embodiment, the PI3K inhibitor is an isoquinolinone. In oneembodiment, the PI3K inhibitor is IPI-145 or a derivative thereof. Inother embodiments, the PI3K inhibitor is INK1117 or a derivativethereof.

In some embodiments, provided herein is a method for using the compoundsor pharmaceutical composition in combination with radiation therapy ininhibiting abnormal cell growth or treating the hyperproliferativedisorder in the subject. Techniques for administering radiation therapyare known in the art, and these techniques can be used in thecombination therapy described herein. The administration of the compoundas disclosed herein in this combination therapy can be determined asdescribed herein.

Radiation therapy can be administered through one of several methods, ora combination of methods, including without limitation external-beamtherapy, internal radiation therapy, implant radiation, stereotacticradiosurgery, systemic radiation therapy, radiotherapy and permanent ortemporary interstitial brachytherapy. The term “brachytherapy,” as usedherein, refers to radiation therapy delivered by a spatially confinedradioactive material inserted into the body at or near a tumor or otherproliferative tissue disease site. The term is intended withoutlimitation to include exposure to radioactive isotopes (e.g., At-211,I-131, I-125, Y-90, Re-186, Re-188, Sm-153, Bi-212, P-32, andradioactive isotopes of Lu). Suitable radiation sources for use as acell conditioner as disclosed herein include both solids and liquids. Byway of non-limiting example, the radiation source can be a radionuclide,such as I-125, I-131, Yb-169, Ir-192 as a solid source, I-125 as a solidsource, or other radionuclides that emit photons, beta particles, gammaradiation, or other therapeutic rays. The radioactive material can alsobe a fluid made from any solution of radionuclide(s), e.g., a solutionof I-125 or I-131, or a radioactive fluid can be produced using a slurryof a suitable fluid containing small particles of solid radionuclides,such as Au-198, Y-90. Moreover, the radionuclide(s) can be embodied in agel or radioactive micro spheres.

Without being limited by any theory, the compounds as disclosed hereincan render abnormal cells more sensitive to treatment with radiation forpurposes of killing and/or inhibiting the growth of such cells.Accordingly, provided herein is a method for sensitizing abnormal cellsin a subject to treatment with radiation which comprises administeringto the subject an amount of a compound as disclosed herein orpharmaceutically acceptable forms, salt, ester, prodrug, or derivativethereof, which amount is effective is sensitizing abnormal cells totreatment with radiation. The amount of the compound, form, salt in thismethod can be determined according to the means for ascertainingeffective amounts of such compounds described herein.

The compounds or pharmaceutical compositions as disclosed herein can beused in combination with an amount of one or more substances selectedfrom anti-angiogenesis agents, signal transduction inhibitors, andantiproliferative agents, glycolysis inhibitors, or autophagyinhibitors.

Anti-angiogenesis agents, such as MMP-2 (matrix-metalloproteinase 2)inhibitors, MMP-9 (matrix-metalloprotienase 9) inhibitors, and COX-11(cyclooxygenase 11) inhibitors, can be used in conjunction with acompound as disclosed herein and pharmaceutical compositions describedherein. Anti-angiogenesis agents include, for example, rapamycin,temsirolimus (CCI-779), everolimus (RAD001), sorafenib, sunitinib, andbevacizumab. Examples of useful COX-II inhibitors include CELEBREX™(alecoxib), valdecoxib, and rofecoxib. Examples of useful matrixmetalloproteinase inhibitors are described in WO 96/33172 (publishedOct. 24, 1996), WO 96/27583 (published Mar. 7, 1996), European PatentApplication No. 97304971.1 (filed Jul. 8, 1997), European PatentApplication No. 99308617.2 (filed Oct. 29, 1999), WO 98/07697 (publishedFeb. 26, 1998), WO 98/03516 (published Jan. 29, 1998), WO 98/34918(published Aug. 13, 1998), WO 98/34915 (published Aug. 13, 1998), WO98/33768 (published Aug. 6, 1998), WO 98/30566 (published Jul. 16,1998), European Patent Publication 606,046 (published Jul. 13, 1994),European Patent Publication 931, 788 (published Jul. 28, 1999), WO90/05719 (published May 31, 1990), WO 99/52910 (published Oct. 21,1999), WO 99/52889 (published Oct. 21, 1999), WO 99/29667 (publishedJun. 17, 1999), PCT International Application No. PCT/IB98/01113 (filedJul. 21, 1998), European Patent Application No. 99302232.1 (filed Mar.25, 1999), Great Britain Patent Application No. 9912961.1 (filed Jun. 3,1999), U.S. Provisional Application No. 60/148,464 (filed Aug. 12,1999), U.S. Pat. No. 5,863,949 (issued Jan. 26, 1999), U.S. Pat. No.5,861,510 (issued Jan. 19, 1999), and European Patent Publication780,386 (published Jun. 25, 1997), all of which are incorporated hereinin their entireties by reference. In some embodiments, MMP-2 and MMP-9inhibitors are those that have little or no activity inhibiting MMP-1.Other embodiments include those that selectively inhibit MMP-2 and/orAMP-9 relative to the other matrix-metalloproteinases (i.e., MAP-1,MMP-3, MMP-4, MMP-5, MMP-6, MMP-7, MMP-8, MMP-10, MMP-11, MMP-12, andMMP-13). Some non-limiting examples of MMP inhibitors are AG-3340, RO32-3555, and RS 13-0830.

Autophagy inhibitors include, but are not limited to, chloroquine,3-methyladenine, hydroxychloroquine (Plaquenil™), bafilomycin A1,5-amino-4-imidazole carboxamide riboside (AICAR), okadaic acid,autophagy-suppressive algal toxins which inhibit protein phosphatases oftype 2A or type 1, analogues of cAMP, and drugs which elevate cAMPlevels such as adenosine, LY204002, N6-mercaptopurine riboside, andvinblastine. In addition, antisense or siRNA that inhibits expression ofproteins including but not limited to ATGS (which are implicated inautophagy), can also be used.

In some embodiments, disclosed herein is a method of and/or apharmaceutical composition for treating a cardiovascular disease in asubject which comprises an amount of a compound as disclosed herein, ora pharmaceutically acceptable form, salt, ester, prodrug or derivativethereof, or an isotopically-labeled derivative thereof, and an amount ofone or more therapeutic agents use for the treatment of cardiovasculardiseases.

Exemplary agents for use in cardiovascular disease applications areanti-thrombotic agents, e.g., prostacyclin and salicylates, thrombolyticagents, e.g., streptokinase, urokinase, tissue plasminogen activator(TPA) and anisoylated plasminogen-streptokinase activator complex(APSAC), anti-platelets agents, e.g., acetyl-salicylic acid (ASA) andclopidrogel, vasodilating agents, e.g., nitrates, calcium channelblocking drugs, anti-proliferative agents, e.g., colchicine andalkylating agents, intercalating agents, growth modulating factors suchas interleukins, transformation growth factor-beta and congeners ofplatelet derived growth factor, monoclonal antibodies directed againstgrowth factors, anti-inflammatory agents, both steroidal andnon-steroidal, and other agents that can modulate vessel tone, function,arteriosclerosis, and the healing response to vessel or organ injurypost intervention. Antibiotics can also be included in combinations orcoatings. Moreover, a coating can be used to effect therapeutic deliveryfocally within the vessel wall. By incorporation of the active agent ina swellable polymer, the active agent will be released upon swelling ofthe polymer.

The compounds described herein can be formulated or administered inconjunction with liquid or solid tissue barriers also known aslubricants. Examples of tissue barriers include, but are not limited to,polysaccharides, polyglycans, seprafilm, interceed and hyaluronic acid.

Medicaments which can be administered in conjunction with the compoundsdescribed herein include any suitable drugs usefully delivered byinhalation for example, analgesics, e.g., codeine, dihydromorphine,ergotamine, fentanyl or morphine; anginal preparations, e.g., diltiazem;antiallergics, e.g. cromoglycate, ketotifen or nedocromil;anti-infectives, e.g., cephalosporins, penicillins, streptomycin,sulphonamides, tetracyclines or pentamidine; antihistamines, e.g.,methapyrilene; anti-inflammatories, e.g., beclomethasone, flunisolide,budesonide, tipredane, triamcinolone acetonide or fluticasone;antitussives, e.g., noscapine; bronchodilators, e.g., ephedrine,adrenaline, fenoterol, formoterol, isoprenaline, metaproterenol,phenylephrine, phenylpropanolamine, pirbuterol, reproterol, rimiterol,salbutamol, salmeterol, terbutalin, isoetharine, tulobuterol,orciprenaline or(−)-4-amino-3,5-dichloro-α-[[[6-[2-(2-pyridinyl)ethoxy]hexyl]-amino]methyl]benzenemethanol;diuretics, e.g., amiloride; anticholinergics e.g., ipratropium, atropineor oxitropium; hormones, e.g., cortisone, hydrocortisone orprednisolone; xanthines e.g., aminophylline, choline theophyllinate,lysine theophyllinate or theophylline; and therapeutic proteins andpeptides, e.g., insulin or glucagon. It will be clear to a personskilled in the art that, where appropriate, the medicaments can be usedin the form of salts (e.g., as alkali metal or amine salts or as acidaddition salts) or as esters (e.g., lower alkyl esters) to optimize theactivity and/or stability of the medicament.

Other exemplary therapeutic agents useful for a combination therapyinclude, but are not limited to, agents as described above, radiationtherapy, hormone antagonists, hormones and their releasing factors,thyroid and antithyroid drugs, estrogens and progestins, androgens,adrenocorticotropic hormone; adrenocortical steroids and their syntheticanalogs; inhibitors of the synthesis and actions of adrenocorticalhormones, insulin, oral hypoglycemic agents, and the pharmacology of theendocrine pancreas, agents affecting calcification and bone turnover:calcium, phosphate, parathyroid hormone, vitamin D, calcitonin, vitaminssuch as water-soluble vitamins, vitamin B complex, ascorbic acid,fat-soluble vitamins, vitamins A, K, and E, growth factors, cytokines,chemokines, muscarinic receptor agonists and antagonists;anticholinesterase agents; agents acting at the neuromuscular junctionand/or autonomic ganglia; catecholamines, sympathomimetic drugs, andadrenergic receptor agonists or antagonists; and 5-hydroxytryptamine(5-HT, serotonin) receptor agonists and antagonists.

Therapeutic agents can also include agents for pain and inflammationsuch as histamine and histamine antagonists, bradykinin and bradykininantagonists, 5-hydroxytryptamine (serotonin), lipid substances that aregenerated by biotransformation of the products of the selectivehydrolysis of membrane phospholipids, eicosanoids, prostaglandins,thromboxanes, leukotrienes, aspirin, nonsteroidal anti-inflammatoryagents, analgesic-antipyretic agents, agents that inhibit the synthesisof prostaglandins and thromboxanes, selective inhibitors of theinducible cyclooxygenase, selective inhibitors of the induciblecyclooxygenase-2, autacoids, paracrine hormones, somatostatin, gastrin,cytokines that mediate interactions involved in humoral and cellularimmune responses, lipid-derived autacoids, eicosanoids, β-adrenergicagonists, ipratropium, glucocorticoids, methylxanthines, sodium channelblockers, opioid receptor agonists, calcium channel blockers, membranestabilizers and leukotriene inhibitors.

Additional therapeutic agents contemplated herein include diuretics,vasopressin, agents affecting the renal conservation of water, rennin,angiotensin, agents useful in the treatment of myocardial ischemia,anti-hypertensive agents, angiotensin converting enzyme inhibitors,β-adrenergic receptor antagonists, agents for the treatment ofhypercholesterolemia, and agents for the treatment of dyslipidemia.

Other therapeutic agents contemplated herein include drugs used forcontrol of gastric acidity, agents for the treatment of peptic ulcers,agents for the treatment of gastroesophageal reflux disease, prokineticagents, antiemetics, agents used in irritable bowel syndrome, agentsused for diarrhea, agents used for constipation, agents used forinflammatory bowel disease, agents used for biliary disease, agents usedfor pancreatic disease. Therapeutic agents include, but are not limitedto, those used to treat protozoan infections, drugs used to treatMalaria, Amebiasis, Giardiasis, Trichomoniasis, Trypanosomiasis, and/orLeishmaniasis, and/or drugs used in the chemotherapy of helminthiasis.Other therapeutic agents include, but are not limited to, antimicrobialagents, sulfonamides, trimethoprim-sulfamethoxazole quinolones, andagents for urinary tract infections, penicillins, cephalosporins, andother, β-Lactam antibiotics, an agent containing an aminoglycoside,protein synthesis inhibitors, drugs used in the chemotherapy oftuberculosis, mycobacterium avium complex disease, and leprosy,antifungal agents, antiviral agents including nonretroviral agents andantiretroviral agents.

Examples of therapeutic antibodies that can be combined with a subjectcompound include but are not limited to anti-receptor tyrosine kinaseantibodies (cetuximab, panitumumab, trastuzumab), anti CD20 antibodies(rituximab, tositumomab), and other antibodies such as alemtuzumab,bevacizumab, and gemtuzumab.

Moreover, therapeutic agents used for immunomodulation, such asimmunomodulators, immunosuppressive agents, tolerogens, andimmunostimulants are contemplated by the methods herein. In addition,therapeutic agents acting on the blood and the blood-forming organs,hematopoietic agents, growth factors, minerals, and vitamins,anticoagulant, thrombolytic, and antiplatelet drugs.

For treating renal carcinoma, one can combine a compound as disclosedherein with sorafenib and/or avastin. For treating an endometrialdisorder, one can combine a compound as disclosed herein withdoxorubincin, taxotere (taxol), and/or cisplatin (carboplatin). Fortreating ovarian cancer, one can combine a compound as disclosed hereinwith cisplatin (carboplatin), taxotere, doxorubincin, topotecan, and/ortamoxifen. For treating breast cancer, one can combine a compound asdisclosed herein with taxotere (taxol), gemcitabine (capecitabine),tamoxifen, letrozole, tarceva, lapatinib, PD0325901, avastin, herceptin,OSI-906, and/or OSI-930. For treating lung cancer, one can combine acompound as disclosed herein with taxotere (taxol), gemcitabine,cisplatin, pemetrexed, Tarceva, PD0325901, and/or avastin.

Further therapeutic agents that can be combined with a subject compoundcan be found in Goodman and Gilman's “The Pharmacological Basis ofTherapeutics” Tenth Edition edited by Hardman, Limbird and Gilman or thePhysician's Desk Reference, both of which are incorporated herein byreference in their entirety.

The compounds described herein can be used in combination with theagents disclosed herein or other suitable agents, depending on thecondition being treated. Hence, in some embodiments, the compounds asdisclosed herein will be co-administered with other agents as describedabove. When used in combination therapy, the compounds described hereincan be administered with the second agent simultaneously or separately.This administration in combination can include simultaneousadministration of the two agents in the same dosage form, simultaneousadministration in separate dosage forms, and separate administration.That is, a compound described herein and any of the agents describedabove can be formulated together in the same dosage form andadministered simultaneously. Alternatively, a compound as disclosedherein and any of the agents described above can be simultaneouslyadministered, wherein both the agents are present in separateformulations. In another alternative, a compound as disclosed herein canbe administered just followed by and any of the agents described above,or vice versa. In the separate administration protocol, a compound asdisclosed herein and any of the agents described above can beadministered a few minutes apart, or a few hours apart, or a few daysapart.

Administration of the compounds as disclosed herein can be effected byany method that enables delivery of the compounds to the site of action.An effective amount of a compound as disclosed herein can beadministered in either single or multiple doses by any of the acceptedmodes of administration of agents having similar utilities, includingrectal, buccal, intranasal and transdermal routes, by intra-arterialinjection, intravenously, intraperitoneally, parenterally,intramuscularly, subcutaneously, orally, topically, as an inhalant, orvia an impregnated or coated device such as a stent, for example, or anartery-inserted cylindrical polymer.

When a compound as disclosed herein is administered in a pharmaceuticalcomposition that comprises one or more agents, and the agent has ashorter half-life than the compound as disclosed herein, unit dose formsof the agent and the compound as disclosed herein can be adjustedaccordingly.

The examples and preparations provided below further illustrate andexemplify the compounds as disclosed herein and methods of preparingsuch compounds. It is to be understood that the scope of the presentdisclosure is not limited in any way by the scope of the followingexamples and preparations. In the following examples molecules with asingle chiral center, unless otherwise noted, exist as a racemicmixture. Those molecules with two or more chiral centers, unlessotherwise noted, exist as a racemic mixture of diastereomers. Singleenantiomers/diastereomers can be obtained by methods known to thoseskilled in the art.

EXAMPLES Biological Activity Assessment

The activity of the compounds as described herein can be determined bythe following procedure, as well as the procedures described in theexamples below. The activity of the kinase is assessed by measuring theincorporation of γ-³³P-phosphate from γ-³³P-ATP onto N-terminal Histagged substrate, which is expressed in E. coli and is purified byconventional methods, in the presence of the kinase. The assay iscarried out in 96-well polypropylene plate. The incubation mixture (100,μL) comprises of 25 mM Hepes, pH 7.4, 10 mM MgCl₂, 5 mMβ-glycerolphosphate, 100 μM Na-orthovanadate, 5 mM DTT, 5 nM kinase, and1 μM substrate Inhibitors are suspended in DMSO, and all reactions,including controls are performed at a final concentration of 1% DMSO.Reactions are initiated by the addition of 10 μM ATP (with 0.5 μCiγ-³³P-ATP/well) and incubated at ambient temperature for 45 minutes.Equal volume of 25% TCA is added to stop the reaction and precipitatethe proteins. Precipitated proteins are trapped onto glass fiber Bfilterplates, and excess labeled ATP washed off using a Tomtec MACH IIIharvestor. Plates are allowed to air-dry prior to adding 30 μL/well ofPackard Microscint 20, and plates are counted using a Packard TopCount.

Chemical Examples

The chemical entities described herein can be synthesized according toone or more illustrative schemes herein and/or techniques well known inthe art.

Unless specified to the contrary, the reactions described herein takeplace at atmospheric pressure, generally within a temperature range from−10° C. to 200° C. Further, except as otherwise specified, reactiontimes and conditions are intended to be approximate, e.g., taking placeat about atmospheric pressure within a temperature range of about −10°C. to about 110° C. over a period that is, for example, about 1 to about24 hours; reactions left to run overnight in some embodiments canaverage a period of about 16 hours.

The terms “solvent,” “organic solvent,” or “inert solvent” each mean asolvent inert under the conditions of the reaction being described inconjunction therewith including, for example, benzene, toluene,acetonitrile, tetrahydrofuran (“THF”), dimethylformamide (“DMF”),chloroform, methylene chloride (or dichloromethane), diethyl ether,methanol, N-methylpyrrolidone (“NMP”), pyridine and the like. Unlessspecified to the contrary, the solvents used in the reactions describedherein are inert organic solvents. Unless specified to the contrary, foreach gram of the limiting reagent, one cc (or mL) of solvent constitutesa volume equivalent.

Isolation and purification of the chemical entities and intermediatesdescribed herein can be effected, if desired, by any suitable separationor purification procedure such as, for example, filtration, extraction,crystallization, column chromatography, thin-layer chromatography orthick-layer chromatography, or a combination of these procedures.Specific illustrations of suitable separation and isolation proceduresare given by reference to the examples hereinbelow. However, otherequivalent separation or isolation procedures can also be used.

When desired, the (R)- and (S)-isomers of the non-limiting exemplarycompounds, if present, can be resolved by methods known to those skilledin the art, for example by formation of diastereoisomeric salts orcomplexes which can be separated, for example, by crystallization; viaformation of diastereoisomeric derivatives which can be separated, forexample, by crystallization, gas-liquid or liquid chromatography;selective reaction of one enantiomer with an enantiomer-specificreagent, for example enzymatic oxidation or reduction, followed byseparation of the modified and unmodified enantiomers; or gas-liquid orliquid chromatography in a chiral environment, for example on a chiralsupport, such as silica with a bound chiral ligand or in the presence ofa chiral solvent. Alternatively, a specific enantiomer can besynthesized by asymmetric synthesis using optically active reagents,substrates, catalysts or solvents, or by converting one enantiomer tothe other by asymmetric transformation.

The compounds described herein can be optionally contacted with apharmaceutically acceptable acid to form the corresponding acid additionsalts. Also, the compounds described herein can be optionally contactedwith a pharmaceutically acceptable base to form the corresponding basicaddition salts.

In some embodiments, disclosed compounds can generally be synthesized byan appropriate combination of generally well known synthetic methods.Techniques useful in synthesizing these chemical entities are bothreadily apparent and accessible to those of skill in the relevant art,based on the instant disclosure. Many of the optionally substitutedstarting compounds and other reactants are commercially available, e.g.,from Aldrich Chemical Company (Milwaukee, Wis.) or can be readilyprepared by those skilled in the art using commonly employed syntheticmethodology.

The discussion below is offered to illustrate certain of the diversemethods available for use in making the disclosed compounds and is notintended to limit the scope of reactions or reaction sequences that canbe used in preparing the compounds provided herein.

General Synthetic Methods

General Method for the Synthesis of Cl—W_(d) heterocycles:

General Conditions for the Preparation of6-chloro-9-(tetrahydro-2H-pyran-2-yl)-9H-purines

To a solution of a given 6-chloro-9H-purine (A-1) (1.29 mol, 1 eq) andTsOH (0.02 mol, 0.015 eq) in ethyl acetate (1000 mL),3,4-dihydro-2H-pyran (1.94 mol, 1.5 eq) is added and the resultingmixture is stirred at reflux for 2 h. The reaction mixture is allowed tocool to RT, aqueous Na₂CO₃ solution (3%, 500 mL) is added and theresulting mixture is stirred for 10 min. The organic layer is separated,washed with water (500 mL×2) and brine (500 mL), dried over anhydrousNa₂SO₄, and filtered. The filtrate is concentrated in vacuo. The productis dissolved in ethyl acetate (50 mL), and then n-heptane (500 mL) isadded. The resulting mixture is stirred at RT for 1 h. The precipitateis collected by filtration, rinsed with heptane (100 mL) and dried invacuo to afford the product6-chloro-9-(tetrahydro-2H-pyran-2-yl)-9H-purine (A-2) as a yellowishsolid.

General Conditions for the Preparation of 4-chloro-1,3,5-triazin-2-amine

2,4-Dichloro-1,3,5-triazine (B-1) (500 mg, 3.3 mmol, 1.0 eq) isdissolved in concentrated ammonium hydroxide (100 mL, 700 mmol, 212 eq)at −20° C. and the resulting mixture is stirred at this temperature for10 min. The mixture is then filtered, rinsed with water (5 mL×3) anddried in vacuo to afford the product, 4-chloro-1,3,5-triazin-2-amine(B-2) as a solid.

General Conditions for the Preparation of4-chloroimidazo[1,2-f][1,2,4]triazine

To a stirred solution of trichloroacetonitrile (28.8 g, 200 mmol, 1 eq)in anhydrous THF (70 mL) at −60° C. under an argon atmosphere,2,2-dimethoxyethanamine (C-1) (21.8 mL, 200 mmol, 1.0 eq) is addeddropwise over 5 min. The resulting mixture is allowed to warm to RT andstirred at RT for 4 h. The mixture is concentrated in vacuo and theresidue is added in portions to a stirred solution of trifluoroaceticacid (100 mL) at −30° C. under argon. The resulting mixture is thenstirred from −30° C. to RT overnight. The reaction mixture isconcentrated in vacuo to afford the product,2-(trichloromethyl)-1H-imidazole (C-2). The product is used in the nextstep without further purification.

The above-obtained residue (C-2) is dissolved in EtOH (300 mL). To thissolution, conc. H₂SO₄ (98%, 30 mL, 522 mmol, 2.76 eq) is added dropwisewhile keeping the reaction temperature below 25° C. The resultingmixture is stirred at reflux for 7 h and then stirred at RT overnight.The mixture is concentrated in vacuo to remove EtOH. The resultingsuspension is diluted with ice-water (200 mL) and neutralized withconcentrated ammonium hydroxide to adjust the pH to 5-6 while keepingthe temperature below 5° C. The solid is collected by filtration, rinsedwith water (10 mL×3), and dried in vacuo to afford a first portion ofthe product. The filtrate is extracted with ethyl acetate (200 mL×2).The combined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo. The resulting residueis combined with the first portion of product and then recrystallized inisopropyl ether to afford the product, ethyl 1H-imidazole-2-carboxylate(C-3).

To a stirred solution of hydroxylamine-o-sulfonic acid (26.64 g, 235.8mmol, 3.0 eq) in H₂O (17 mL) at 0° C., ethyl 1H-imidazole-2-carboxylate(C-3) (11.0 g, 78.6 mmol, 1.0 eq) is added and the resulting mixture isstirred at 90° C. for 30 min. The mixture is cooled to RT and K₂CO₃ (3.6g, 26.2 mmol, 1.0 eq) is added in portions. The resulting mixture isstirred at RT overnight, filtered and rinsed with H₂O (10 mL×3). Thefiltrate is extracted with ethyl acetate (50 mL×5). The combined organiclayer is washed with brine, dried over Na₂SO₄ and filtered. The filtrateis evaporated in vacuo and the residue is purified by flash columnchromatography on silica gel (1% MeOH-DCM) to afford the product, ethyl1-amino-1H-imidazole-2-carboxylate (C-4) as a colorless oil.

A mixture of ethyl 1-amino-1H-imidazole-2-carboxylate (C-4) (800 mg,5.16 mmol, 1.0 eq) and formamidine acetate (2.68 g, 25.78 mmol, 5.0 eq)in EtOH (100 mL) is stirred at reflux overnight. The resulting mixtureis cooled to RT. The solid is collected by filtration, rinsed with EtOH(3×2 mL) and petroleum ether (2 mL×3), and then dried in vacuo to affordthe product, imidazo[1,2-f][1,2,4]triazin-4-ol (C-5).

Imidazo[1,2-f][1,2,4]triazin-4-ol (C-5) (400 mg, 2.94 mmol, 1.0 eq) isdissolved in POCl₃ (10 mL, 109.2 mmol, 37.1 eq) and the resultingmixture is stirred at reflux for 2 h. The mixture is concentrated invacuo to remove POCl₃. The residue is poured into ice water (30 mL) andneutralized with saturated aqueous NaHCO₃ solution to adjust the pH to6-7 while keeping the temperature below 5° C. The mixture is extractedwith ethyl acetate (30 mL×4). The combined organic layers are washedwith brine, dried over Na₂SO₄ and filtered. The filtrate is concentratedin vacuo and the residue is purified by flash column chromatography onsilica gel (16% ethyl acetate in petro ether) to afford the product,4-chloroimidazo[1,2-f][1,2,4]triazine (C-6).

General Conditions for the Preparation of4-chloroimidazo[1,5-f][1,2,4]triazine

4-Chloroimidazo[1,5-f][1,2,4]triazine (D-4) is prepared fromcommercially available material (D-1) through a three-step sequence inanalogous fashion to the synthesis of4-chloroimidazo[1,2-f][1,2,4]triazine (C-6) from compound (C-3B) inMethod C.

General Method for the Synthesis of4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile

To a suspension of 4-chloro-7H-pyrrolo[2,3-d]pyrimidine (E-1) (3.99 g,26.0 mmol, 1.0 eq) in dry DCM (150 mL) under argon, N-bromosuccinimide(6.02 g, 33.8 mmol, 1.3 eq) is added and the resulting mixture isstirred at RT for 3 h. The reaction mixture is diluted with MeOH (30 mL)and then concentrated in vacuo to yield a slight brown solid. Theresidue is triturated with H₂O (150 mL). The solid is collected byfiltration and then re-crystallized in MeOH to afford the product,5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (E-2).

To a solution of 5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (E-2)(2.33 g, 10.0 mmol, 1.0 eq) in anhydrous THF (100 mL) at −78° C. underargon, n-BuLi solution (2.5 M in THF, 8.8 mL, 22.0 mmol, 2.2 eq) isadded dropwise (over 10 min). The resulting mixture is stirred at −78°C. for 1 h and then DMF (2.0 g, 11.0 mmol, 1.1 eq) is added dropwise(over 10 min). The mixture is stirred at −78° C. for an additional 30min and then stirred at RT overnight. The reaction mixture is quenchedwith H₂O (50 mL) and then concentrated in vacuo. The residue istriturated with saturated aqueous NH₄Cl solution. The solid is collectedby filtration, rinsed with ethyl acetate, and dried in vacuo to affordthe product, 4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehyde (E-3).

To a suspension of 4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehyde(E-3) (1.17 g, 6.47 mmol, 1.0 eq) and hydroxylamine hydrochloride (0.54g, 7.77 mmol, 1.2 eq) in EtOH (25 mL), aqueous NaOH solution (0.31 g,7.77 mmol, 1.2 eq) in H₂O (4 mL) is added dropwise. The resultingmixture is stirred at RT for 30 min and then is diluted with asufficient amount of EtOH to allow stirring for additional 30 min. Thesolid is collected by filtration, rinsed with H₂O and dried in vacuo toafford the product, 4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehydeoxime (E-4) as a mixture of isomers.

To a suspension of 4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehydeoxime (E-4) (865 mg, 4.40 mmol, 1.0 eq) in DCM (20 mL), thionyl chloride(3.1 mL, 43.7 mmol, 10.0 eq) is added and the resulting mixture isstirred at RT overnight. The reaction mixture is concentrated in vacuo.The residue is suspended in water (60 mL) and saturated aqueous NaHCO₃is added to adjust the pH to 4. The solid is collected by filtration,rinsed with water followed by ethyl acetate to afford a first portion ofproduct. The filtrate is then extracted with ethyl acetate (50 mL×3).The combined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo and the residue iscombined with the first portion of product. The product is thenre-crystallized in ethyl acetate/hexanes (1:1) and dried in vacuo toafford the final product,4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (E-5) as a palesolid.

General Method for the Synthesis of4-chloro-5-fluoro-7H-pyrrolo[2,3-d]pyrimidine

4-Chloro-7H-pyrrolo[2,3-d]pyrimidine (E-1) (5.01 g, 32.6 mmol, 1 eq) andSelectfluor (17.32 g, 48.9 mmol, 1.5 eq) are dissolved in a mixture ofdry acetonitrile (250 mL) and AcOH (50 mL). The resulting mixture isstirred at 70° C. under argon for 16 h. The mixture is concentrated invacuo. The residue is dissolved in a mixture of DCM-ethyl acetate (1:1,50 mL) and filtered through celite. The filtrate is concentrated invacuo and the residue is purified by flash chromatography on silica gel(0-0.7% MeOH-DCM) to afford the product,4-chloro-5-fluoro-7H-pyrrolo[2,3-d]pyrimidine (F-1) as a pink solid.

General Method for the Synthesis of4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide

To a mixture of 5-bromo-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (E-2) (6.24g, 26.8 mmol, 1.0 eq) in anhydrous THF (100 mL) at 78° C. under argon,n-BuLi solution (2.5 M in THF, 23.6 mL, 59.0 mmol, 2.2 eq) is addeddropwise (over 30 min). The reaction mixture is then stirred at −78° C.for 1 h and then dry ice (300 g) is added in portions under an argonatmosphere. The resulting mixture is allowed to warm to RT and thenstirred at RT overnight. The reaction mixture is then diluted with H₂O(200 mL) and extracted with ethyl acetate (50 mL×4). The aqueous layeris acidified with con. HCl to adjust the pH to 3-4. The precipitate isthen collected by filtration, rinsed with H₂O (30 mL) and dried in vacuoto afford the product, 4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylicacid (G-1).

To a stirred suspension of4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid (G-1) (3.11 g,15.7 mmol, 1.0 eq) and a catalytic amount of DMF in a mixture of DCM (40mL) and THF (40 mL) at RT, oxalyl dichloride (2.0 mL, 23.5 mmol, 1.5 eq)is added dropwise. The resulting mixture is stirred for 2 h and thenconcentrated in vacuo. The residue (G2) is dissolved in DCM (50 mL) andthe resulting solution is added dropwise to saturated aqueous ammoniumhydroxide (200 mL) at RT. The resulting mixture is stirred for 30 minand then filtered. The filter cake is then rinsed with H₂O (30 mL×2).The filtrate is acidified with con. HCl to adjust the pH to 4-5. Thesolid is collected by filtration, rinsed with water and dried in vacuoto afford the product,4-chloro-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide (G-3).

General Method for the Synthesis of4-chloro-5-(trifluoromethyl)pyrimidin-2-amine

Ammonia in methanol (7N solution, 15 mL) is added dropwise to thestirred neat 2,4-dichloro-5-(trifluoromethyl)pyrimidine (H-1) (5.0 g,23.04 mmol) under argon, and the resulting mixture is stirred at RT for2 h. The reaction mixture is quenched with water and then extracted withethyl acetate (200 mL×2). The combined organic layers are washed withbrine, dried over Na₂SO₄ and filtered. The filtrate is concentrated invacuo and the residue is purified by flash chromatography on silica gel(0-20% ethyl acetate-hexanes) to afford the product,4-chloro-5-(trifluoromethyl)pyrimidin-2-amine (H-2) as a white solid.The regional-isomer, 2-chloro-5-(trifluoromethyl)pyrimidin-4-amine (H-3)can also be isolated as a white solid.

General Method for the Synthesis of Amine Cores

General Conditions for the Preparation of(S)-3-(1-aminoethyl)-isoquinolin-1(2H)-ones

To a stirred mixture of a given o-methylbenzoic acid (I-1) (1.5 mol, 1eq) and DMF (2 mL) in DCM (1275 mL) at RT, oxalyl chloride (1.65 mol,1.1 eq) is added over 5 min and the resulting mixture is stirred at RTfor 2 h. The mixture is then concentrated in vacuo. The residue isdissolved in DCM (150 mL) and the resulting solution (solution A) isused directly in the next step.

To a stirred mixture of aniline (1.58 mol, 1.05 eq) and triethylamine(3.15 mol, 2.1 eq) in DCM (1350 mL), the above solution A (150 mL) isadded dropwise while the reaction temperature is maintained between 25°C. to 40° C. by an ice-water bath. The resulting mixture is stirred atRT for 2 h and then water (1000 mL) was added. The organic layers areseparated and washed with water (1000 mL×2), dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo. The product issuspended in n-heptanes (1000 mL) and stirred at RT for 30 min. Theprecipitate is collected by filtration, rinsed with heptanes (500 mL)and further dried in vacuo to afford the amide (I-2) as a yellow solid.

To a stirred mixture of amide (I-2) (173 mmol, 1 eq) in anhydrous THF(250 mL) at −30° C. under an argon atmosphere, a solution ofn-butyllithium in hexanes (432 mol, 2.5 eq) is added dropwise over 30min while keeping inner temperature between −30° C. and −10° C. Theresulting mixture is then stirred at −30° C. for 30 min.

To a stirred mixture of (S)-tert-butyl1-(methoxy(methyl)amino)-1-oxopropan-2-ylcarbamate (260 mmol, 1.5 eq) inanhydrous THF (250 mL) at −30° C. under an argon atmosphere, a solutionof isopropylmagnesium chloride in THF (286 mmol, 1.65 eq) is addeddropwise over 30 min while keeping inner temperature between −30° C. and−10° C. The resulting mixture is stirred at −30° C. for 30 min. Thissolution is then slowly added to above reaction mixture while keepinginner temperature between −30° C. and −10° C. The resulting mixture isstirred at −15° C. for 1 h. The reaction mixture is quenched with water(50 mL) and then acidified with conc. HCl at −10° C.-0° C. to adjust thepH to 1-3. The mixture is allowed to warm to RT and concentrated invacuo. The residue is dissolved in MeOH (480 mL), and then conc. HCl(240 mL) is added quickly at RT. The resulting mixture is stirred atreflux for 1 h. The reaction mixture is concentrated in vacuo to reducethe volume to about 450 mL. The residue is extracted with a 2:1 mixtureof heptane and ethyl acetate (500 mL×2). The aqueous layer is basifiedwith concentrated ammonium hydroxide to adjust the pH value to 9-10while keeping the inner temperature between −10° C. and 0° C. Themixture is then extracted with DCM (300 mL×3), washed with brine, driedover MgSO₄ and filtered. The filtrate is concentrated in vacuo and theresidue is dissolved in MeOH (1200 mL) at RT. To this solution,D-(−)-tartaric acid (21 g, 140 mmol, 0.8 eq) is added in one portion atRT. After stirring at RT for 30 min, white solid precipitates out andthe mixture is slurried at RT for 10 h. The solid is collected byfiltration and rinsed with MeOH (50 mL×3). The collected solid issuspended in water (500 mL) and then neutralized with concentratedammonium hydroxide solution at RT to adjust the pH to 9-10. The mixtureis extracted with DCM (200 mL×3). The combined organic layers are washedwith brine, dried over MgSO₄ and filtered. The filtrate is concentratedin vacuo to afford (S)-3-(1-aminoethyl)-isoquinolin-1(2H)-ones (I-3).

General Conditions for the Preparation of7-(1-aminoethyl-6-phenyl-1,6-naphthyridin-5(6H)-ones

To a mixture of ethyl 2-cyanoacetate (J-1) (45.2 g, 400 mmol) and agiven ketone (800 mmol) in glacial acetic acid (50 mL), piperidine (2mL, 20 mmol) is added and the resulting mixture is stirred at reflux for24 h. The reaction mixture is allowed to cool to RT, and thenconcentrated in vacuo. The residue is diluted with water (200 mL) andextracted with ethyl acetate (200 mL×3). The combined organic layers arewashed with brine (50 mL), dried over Na₂SO₄ and filtered. The filtrateis concentrated in vacuo and the residue is purified by flash columnchromatography on silica gel (0-2% EA/PE) to afford the product (J-2) asa white solid.

To a solution of (J-2) (285 mol) in absolute EtOH (300 mL),N,N-dimethylformamide dimethyl acetal (37.3 g, 313 mmol) is addeddropwise and the resulting mixture is stirred at reflux 6 h. The mixtureis allowed to cool to RT, and concentrated in vacuo to afford theproduct (J-3) in as a yellow solid. This material is used in the nextstep without further purification.

Dienoate (J-3) (148 mmol) is dissolved in AcOH (120 mL) and the mixtureis stirred at 40° C. A solution of 45% HBr—AcOH (120 mL) is addeddropwise, and then the mixture is stirred at 55° C. for 2 h. The mixtureis allowed to cool to RT, poured onto ice, neutralized with solidNa₂CO₃, and extracted with ethyl acetate (150 mL×3). The combinedorganic layers are washed with brine (50 mL), dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo and the residue ispurified by flash column chromatography on silica gel (5-20% EA/PE) toafford the product (J-4) as a yellow oil.

To a solution of 4-substituted ethyl 2-bromolnicotinate (J-4) (52 mmol)in 1,4-dioxane (15 mL), a solution of NaOH (8.0 g, 200 mmol) in H₂O (15mL) is added and the resulting mixture is stirred at reflux for 12 h.The mixture is allowed to cool to RT, diluted with H₂O, and washed withethyl acetate (30 mL×3). The aqueous layer is acidified withconcentrated hydrochloric acid to pH to 1, and then extracted with ethylacetate (50 mL×3). The combined organic layers are washed with brine (25mL), dried over Na₂SO₄ and filtered. The filtrate is concentrated invacuo to afford the product nicotinic acid (J-5) as a white solid.

To a solution of (J-5) (60 mmol) and DMF (3 drops) in CH₂Cl₂ (150 mL),oxalyl chloride (11.4 g, 90 mmol) is added dropwise and the resultingmixture is stirred at RT for 2 h. The reaction mixture is concentratedin vacuo to afford the nicotinoyl chloride (J-6) as a yellow oil.

To a solution of nicotinoyl chloride (J-6) (23.26 mmol) in anhydrous THF(70 mL) at 0° C., aniline (25.59 mmol) and triethylamine (3.6 mL, 25.59mmol) is added slowly. The resulting mixture is stirred at RT for 1 h.The reaction mixture is quenched with water and extracted with ethylacetate. The combined organic layers are washed with brine, dried overNa₂SO₄ and filtered. The filtrate is concentrated in vacuo to afford theamide (J-7) as a tan solid.

To a solution of nicotinamide (J-7) (6.77 g, 23.25 mmol) andtributyl(vinyl)tin (10.2 mL, 34.88 mmol) in DMF (250 mL) under argon,Pd(PPh₃)₄ (1.07 g, 0.93 mmol) is added and the resulting mixture isstirred at 90° C. for 1 h. The mixture is allowed to cool to RT,quenched with water and extracted with ethyl acetate (100 mL×2). Theorganic layer is washed with brine, dried over Na₂SO₄, and filtered. Thefiltrate is concentrated in vacuo and the residue is purified by ISCO(silica gel cartridge, 0-60% EA/Hexanes) to afford the vinylnicotinamide(J-8) as a red solid.

To a solution of 2-vinylnicotinamide (J-8) (30.21 mmol) in anhydrous DMF(100 mL) at RT, sodium hydride (60% in mineral oil, 6.04 g, 151.08 mmol)is slowly added in portions. The resulting mixture is stirred at RT for45 min. To this mixture, ethyl chloroacetate (16 mL, 151.08 mmol) isadded dropwise and the resulting mixture is stirred for 2 h. Thereaction is quenched with water and extracted with ethyl acetate. Thecombined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo to afford (J-9).

To a solution of (J-9) (17.36 mmol) in 1,4-dioxane-H₂O (3:1, 150 mL) atRT, osmium tetraoxide (4% wt in H₂O, 2.72 mL, 0.35 mmol) is added andthe resulting mixture is stirred at RT for 30 min. To this mixture,sodium periodate (14.85 g, 69.44 mmol) is added and the resultingmixture is stirred at RT for 16 h. The mixture is filtered throughcelite and the filtrate is extracted with ethyl acetate (2×100 mL). Thecombined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo to afford the product(J-10) as a tan/yellow solid.

To a solution of (J-10) (17.35 mmol) in EtOH-ethyl acetate (3:1, 200 mL)is added cesium carbonate (6.22 g, 19.09 mmol) and the resulting mixtureis stirred at 50° C. for 2 h. The mixture is allowed to cool to RT andfiltered through celite. The filtrate is concentrated in vacuo and theresidue is partitioned between water and ethyl acetate. The organiclayer is washed with brine, dried over Na₂SO₄ and filtered. The filtrateis concentrated in vacuo and the residue is purified by ISCO (silica gelcartridge, 0-50% EA/Hex) to afford the product (J-11) as an off whitesolid.

To a solution of (J-11) (6.97 mmol) in anhydrous MeOH (40 mL), sodiumborohydride (2.62 g, 69.34 mmol) is added in two portions. The mixtureis stirred at RT for 16 h, quenched with water and extracted with ethylacetate. The combined organic layers are washed with brine, dried overNa₂SO₄ and filtered. The filtrate is concentrated in vacuo to affordproduct (J-12).

To a solution of (J-12) (13.61 mmol) in anhydrous DCM (50 mL) at RT, 4 Åmolecular sieves (powder, 3.62 g), NMO (1.59 G, 13.6 mmol) and TPAP(tetrapropylammonium perruthenate) (119.5 mg, 0.34 mmol) are addedsequentially. The resulting mixture is stirred at RT for 16 h(overnight). The mixture is filtered through a celite/silica gel pad andthe filtrate is concentrated in vacuo to afford the product (J-13).

To a solution of (J-13) (6.80 mmol) in anhydrous THF (100 mL) at −78° C.under argon, methylmagnesium chloride solution (3.0 M in THF, 6.8 mL,20.41 mmol) is added dropwise and the resulting mixture was stirred from−78° C. to RT for 2 h. An additional amount of methylmagnesium chloridesolution (2 mL) is added to bring reaction to completion. The reactionmixture is quenched with water (150 mL) and extracted with ethyl acetate(200 mL×2). The combined organic layers are washed with brine, driedover Na₂SO₄ and filtered. The filtrate is concentrated in vacuo and theresidue is purified by ISCO (silica gel cartridge, 0-10% MeOH-DCM) toafford the product (J-14) as a white solid.

To a solution of (J-14) (4.28 mmol) in anhydrous THF (25 mL) at 0° C.under argon, triphenyl phosphine (2.24 g, 8.56 mmol) is added and theresulting mixture was stirred for 5 min. To this mixture, diphenylphosphoryl azide (2.31 mL, 10.7 mmol) is added followed by slow additionof diisopropyl azodicarboxylate (1.69 mL, 8.56 mmol) over 20 min periodof time. The resulting mixture is stirred from 0° C. to RT for 2 h. Themixture is then partitioned between ethyl acetate and water. The organiclayer is washed with brine, dried over Na₂SO₄ and filtered. The filtrateis concentrated in vacuo and the residue is purified by ISCO (silica gelcartridge, 0-70% EA/Hex) to afford the product, (J-15) as a white solid.

A mixture of (J-15) (3.08 mmol) and palladium (10% weight on carbon, 190mg, 20% of starting material by weight) in anhydrous MeOH (25 mL) aredegassed and flushed with hydrogen (three cycles). The reaction mixtureis stirred under a hydrogen atmosphere (hydrogen balloon) at RT for 30min. The mixture is then filtered through celite over a Buchner funneland rinsed with ethyl acetate. The filtrate is concentrated in vacuo toafford the product (J-16) as an off-white solid.

General Conditions for the Preparation of3-(1-aminoethyl)-2-phenyl-3,4-dihydroisoquinolin-1(2H)-ones

A mixture of benzoic acid (K-1) (400 mmol), oxalyl chloride (101 g, 800mmol) and DMF (0.2 ml) in DCM (400 mL) is stirred at RT for 2 h. Themixture is concentrated in vacuo to afford the acid chloride (K-2) as ayellow oil. The product obtained is used directly in the next stepwithout purification.

A mixture of aniline (420 mmol) and triethylamine (71 g, 700 mmol) inDCM (300 mL) is stirred at RT for 10 min. To this mixture, acid chloride(K-2) (64 g, 400 mmol) is added dropwise, and the resulting mixture isstirred at RT for 30 min. The reaction mixture is poured into water (300mL) and extracted with DCM (200 mL×3), dried over anhydrous Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo to afford the product.The product is suspended in isopropyl ether (300 mL), stirred at refluxfor 30 min, and then cooled to 0-5° C. The precipitate is collected byfiltration and further dried in vacuo to afford the product amide (K-3)as a yellow solid.

To a stirred solution of amide (K-3) (0.1 mol, 1.0 eq) in anhydrous THF(225 mL) at −78° C. under an argon atmosphere, a solution ofn-butyllithium in hexanes (120 mL, 2.5 M, 0.3 mol, 3 eq) is addeddropwise over 1 h period of time while keeping inner temperature between−78° C. to −50° C. The resulting mixture is stirred at −70° C. for 1 h,and then diethyl oxalate (17.5 g, 0.12 mol, 1.2 eq) is quickly added(with an increase in temperature to −20° C. upon addition). The mixtureis stirred at −50° C. for 10 min, and then quenched with water (100 mL).The inorganic salt is removed by filtration, and the filtrate isextracted with ethyl acetate (100 mL×2). The combined organic layers arewashed with brine (100 mL), dried over MgSO₄ and filtered. The filtrateis concentrated in vacuo to afford the product as a semi-solid. Theproduct is slurried in isopropyl ether (100 mL) at RT for 10 min. Thesolid is collected by filtration and further dried in vacuo to affordthe product (K-4) as a white solid. The product obtained is useddirectly in the next step.

Compound (K-4) (88 mmol, 1 eq) is dissolved in HCl/MeOH (10 M, 100 mL,10 mL/1 g of K-4), and the resulting mixture is stirred at reflux for 1h. The reaction mixture is concentrated in vacuo, and the residue isslurried in ethyl acetate (100 mL) at RT for 30 min. The solid iscollected by filtration, rinsed with ethyl acetate (50 mL×3), andfurther dried in vacuo to afford the product (K-5) as a white solid.

To a stirred suspension of lithium aluminum hydride (15.6 g, 410 mmol)in anhydrous THF (500 mL) at −78° C. under a nitrogen atmosphere, (K-5)(137 mmol) is slowly added over a 10 min period of time. The resultingmixture is allowed to warm to −30° C. and stirred for 30 min (TLC showsthe completion of the reaction). Then the mixture is cooled to −78° C.,and quenched carefully with water (100 mL). The mixture is allowed towarm to RT, filtered through silica gel (20 g), and the filtrate isconcentrated in vacuo. The product is poured into H₂O (200 mL) andextracted with ethyl acetate (200 mL×3). The combined organic layers arewashed with brine (100 mL), dried over Na₂SO₄ and filtered. The filtrateis concentrated in vacuo. The product is suspended in ethyl acetate (30mL) and stirred for 10 min. The solid is collected by filtration andfurther dried in vacuo to afford the product (K-6) as a white solid.

To a stirred solution of oxalyl chloride (2.0 M in DCM, 12.8 mL) inanhydrous DCM (100 mL) at −78° C. under argon, DMSO (4.82 mL, 68 mmol)is slowly added and the resulting mixture is stirred at −78° C. for 50min. To this reaction mixture, a solution of (K-6) (17 mmol) in DCM (50mL) is added slowly. The resulting mixture is stirred at −78° C. for 1 hand then triethylamine (11.8 mL, 85 mmol) is added. The mixture isstirred from −78° C. to RT for 1 h and quenched with water (100 mL). Theorganic layer is separated and the aqueous layer is extracted with DCM(50 mL×2). The combined organic layers are washed with brine, dried overNa₂SO₄ and filtered. The filtrate is concentrated in vacuo to afford theproduct, (K-7).

To a solution of (K-7) (17.0 mmol) in anhydrous THF (120 mL) at −78° C.under argon, methylmagnesium chloride solution (3.0 M in THF, 14.9 mL,44.2 mmol) is added dropwise and the resulting mixture is stirred at−78° C. for 3 h. The mixture is quenched with saturated NH₄Cl aqueoussolution (50 mL) and extracted with ethyl acetate (200 mL×2). Thecombined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo and the residue wastriturated with 20% ethyl aceate-hexanes to afford the product (K-8) asa yellowish solid.

To a solution of (K-8) (7.88 mmol) in anhydrous THF (60 mL) at 0° C.under argon, triphenyl phosphine (3.1 g, 11.81 mmol) is added and theresulting mixture was stirred for 5 min. To this mixture, diphenylphosphoryl azide (3.41 mL, 15.76 mmol) is added followed by slowaddition of diisopropyl azodicarboxylate (2.32 mL, 11.81 mmol) over 20min. The resulting mixture is stirred from 0° C. to RT for 5 h. Themixture is then partitioned between ethyl acetate and water. The organiclayer is washed with brine, dried over Na₂SO₄ and filtered. The filtrateis concentrated in vacuo and the residue is purified by ISCO (silica gelcartridge, 0-100% ethyl acetate/hexanes) to afford the product azide(K-9).

A mixture of azide (K-9) (1.1 mmol) and palladium (10% weight on carbon,100 mg, 30% of starting material by weight) in anhydrous methanol (20mL) is degassed and flushed with hydrogen (three cycles). The reactionmixture is stirred under a hydrogen atmosphere (hydrogen balloon) at RTfor 24 h. The mixture is filtered through celite over a Buchner funneland rinsed with ethyl aceate. The filtrate is concentrated in vacuo toafford the amine (K-10) as a yellow solid.

General Method for the Capping of Amine Cores with Cl—W_(d)

An (S)-3-(1-Aminoethyl)-isoquinolin-1(2H)-one (I-5) (115 mmol, 1.0 eq),Cl-Wd (173 mmol, 1.5 eq) and triethylamine (344 mmol, 3.0 eq) aredissolved in n-BuOH (350 mL) and the mixture is stirred at reflux for 16h. The reaction mixture is cooled to RT and concentrated in vacuo. Theresidue is slurried in a mixture of H₂O (200 mL) and ethyl acetate (100mL) and stirred at RT for 30 min. The solid is then collected byfiltration, rinsed with ethyl acetate (25 mL) and dried in vacuo toafford the product (L-1).

General Method for the Elaboration of W_(d) Heterocycles

A mixture of tetrahydro-2H-pyran-intermediate (M-1) in ethanol (4vol)/water (2 vol) followed by addition of conc. HCl solution (2 vol) isstirred at RT for 1 h. The resulting mixture is diluted with cold water,neutralized with saturated aqueous NaHCO₃ to adjust the pH to 8-9 andthen extracted with DCM (20 vol×3). The combined organic layers arewashed with brine, dried over Na₂SO₄ and filtered. The filtrate isconcentrated in vacuo. The resultant residue is suspended in petroleumether with ultrasonic vibration for 5 min. The solid is collected byfiltration and dried in vacuo to afford the product (M-2).

General Method for the Synthesis of6-chloro-5-(trifluoromethyl)pyrimidin-4-amine

To a rapidly stirred mixture of1,1,1,3-tetrafluoro-2-(trifluoromethyl)-4-oxapent-2-ene (N-1) (10.0 g,47.15 mmol) and formamidine acetate (7.37 g, 70.73 mmol) in a mixture ofwater (50 mL) and dichloromethane (50 mL) at 0° C., a solution of sodiumhydroxide (7.54 g, 189 mmol) in water (40 mL) is added dropwise and theresulting mixture is stirred for 30 min after complete addition. Thedichloromethane layer is separated, washed with 1M aqueous HCl solutionand water, dried over Na₂SO₄ and filtered. The filtrate is concentratedin vacuo to afford 4-fluoro-6-methoxy-5-(trifluoromethyl)pyrimidine(N-2) as a yellow solid. The product is used directly in the next stepwithout further purification.

To a solution of 4-fluoro-6-methoxy-5-(trifluoromethyl)pyrimidine (N-2)(1.10 g, 5.61 mmol) in n-butanol (4 mL) in a pressure vessel, ammoniumhydroxide (5 mL) is added and the resulting mixture is stirred at 90° C.for 1 h. The mixture is allowed to cool to RT, quenched with water, andextracted with ethyl acetate (100 mL×2). The combined organic layers arewashed with brine, dried over Na₂SO₄ and filtered. The filtrate isconcentrated in vacuo to afford the product6-methoxy-5-(trifluoromethyl)pyrimidin-4-amine (N-3) as an off-whitesolid. The product is used directly in the next step without furtherpurification.

To a solution of 6-methoxy-5-(trifluoromethyl)pyrimidin-4-amine (N-3)(420 mg, 2.18 mmol) in 1,4-dioxane (10 mL), concentrated HCl (1.81 mL,21.8 mmol) is added and the resulting mixture is stirred at 90° C. for 3h. The mixture is allowed to cool to RT and then concentrated in vacuoto afford the product, 6-amino-5-(trifluoromethyl)pyrimidin-4-ol (N-4)as yellowish solid.

The mixture of 6-amino-5-(trifluoromethyl)pyrimidin-4-ol (N-4) (300 mg,1.66 mmol) in POCl₃ (8 mL) in a pressure vessel is stirred at 100° C.for 1 h. The mixture is allowed to cool to RT and concentrated in vacuo.The residue is taken up in water (20 mL), basified with saturated NaHCO₃aqueous solution to pH=9 and then extracted with DCM (30 mL x3). Thecombined organic layers are washed with brine, dried over Na₂SO₄ andfiltered. The filtrate is concentrated in vacuo to afford the desiredproduct, 6-chloro-5-(trifluoromethyl)pyrimidin-4-amine (N-5) as a yellowsolid.

Example 1

Isoquinolinone 4 was prepared from compound 1 through a 3-step sequence.Compound 1 was prepared using Method I and was then converted to 2 bycoupling with A-2 according to Method L. Compound 2 was converted tocompound 3 according to Method M. Compound 4 was then prepared accordingto the following procedure:

To a solution of(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-chloro-2-phenylisoquinolin-1(2H)-one(3) (100 mg, 0.24 mmol) in 1,4-dioxane (3 mL) in a sealed tube,pyrrolidine (1.25 mL, excess amount) was added and the resulting mixturewas stirred at 135° C. for 17 h. The mixture was allowed to cool to RT,partitioned between ethyl acetate and water. The organic layer waswashed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo and the residue was purified by ISCO (silica gelcartridge, 0-10% MeOH-DCM) to afford the product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-2-phenyl-8-(pyrrolidin-1-yl)isoquinolin-1(2H)-one(4) as an off-white solid. ESI-MS m/z: 452.2 [M+H]⁺.

Example 2

Isoquinolinone 5 was prepared from compound 3 according to the followingprocedure:

(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-chloro-2-phenylisoquinolin-1(2H)-one(3) (200 mg, 0.48 mmol) and 1-methylpiperazine (0.267 mL, 2.4 mmol) weredissolved in anhydrous NMP (8 mL) and the resulting solution wasdegassed and back-filled with argon (two cycles). To this mixture,Na₂CO₃ (102 mg, 0.96 mmol), Pd(OAc)₂ (11 mg, 0.048 mmol) anddi-(1-adamantyl)-n-butylphosphine (52 mg, 0.144 mmol) were addedsequentially. The resulting mixture was degassed and back-filled withargon (two cycles) and then stirred at 160° C. under argon for 16 h. Thereaction mixture was allowed to cool to RT and then partitioned betweenwater and ethyl acetate. The organic layers were separated and theaqueous layer was extracted with ethyl acetate. The combined organiclayers were washed with brine, dried over Na₂SO₄ and filtered. Thefiltrate was concentrated in vacuo and the residue was purified by ISCO(silica gel cartridge, 0-10% MeOH-DCM with 0.1% TEA) to afford theproduct,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-(4-methylpiperazin-1-yl)-2-phenylisoquinolin-1(2H)-one(5) as a yellowish solid. ESI-MS m/z: 481.2 [M+H]⁺.

Example 3

Isoquinolinone 6 was prepared from compound 3 by coupling with1H-pyrazole-4-boronic acid using the following procedure:

(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-chloro-2-phenylisoquinolin-1(2H)-one(3) (200 mg, 0.48 mmol) and 1H-pyrazole-4-boronic acid (108 mg, 0.96mmol) were dissolved in anhydrous NMP (8 mL) and the resulting solutionwas degassed and back-filled with argon (two cycles). To this mixture,Na₂CO₃ (152 mg, 1.44 mmol), Pd(OAc)₂ (22 mg, 0.096 mmol) anddi-(1-adamantyl)-n-butylphosphine (104 mg, 0.288 mmol) were addedsequentially. The resulting mixture was degassed and back-filled withargon (two cycles) and then stirred at 160° C. under argon for 3 h. Thereaction mixture was allowed to cool to RT and then partitioned betweenwater and ethyl acetate. The organic layer was separated and the aqueouslayer was extracted with ethyl acetate. The combined organic layers werewashed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo and the residue was triturated with Et₂O to affordthe product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-2-phenyl-8-(1H-pyrazol-3-yl)isoquinolin-1(2H)-one(6) as a yellowish solid. ESI-MS m/z: 449.2 [M+H]⁺.

Example 4

Isoquinolinone 7 was prepared from compound 3 in analogous fashion tocompound 6 in Example 3 except that pyridin-3-ylboronic acid was used inplace of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 460.2 [M+H]⁺.

Example 5

Isoquinolinone 8 was prepared from compound 3 according to the followingprocedure:

(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-chloro-2-phenylisoquinolin-1(2H)-one(3) (417 mg, 1.0 mmol) and tributyl(vinyl)tin (0.58 mL, 2.0 mmol) weredissolved in anhydrous NMP (10 mL) and the resulting solution wasdegassed and back-filled with argon (two cycles). To this mixture,Na₂CO₃ (212 mg, 2.0 mmol), Pd(OAc)₂ (45 mg, 0.2 mmol) anddi-(1-adamantyl)-n-butylphosphine (215 mg, 0.6 mmol) were addedsequentially. The resulting mixture was degassed and back-filled withargon (two cycles) and then stirred at 160° C. under argon for 1 h. Thereaction mixture was allowed to cool to RT and then partitioned betweenwater and ethyl acetate. The organic layer was separated and the aqueouslayer was extracted with ethyl acetate. The combined organic layers werewashed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo and the residue was purified by ISCO (silica gelcartridge, 0-10% MeOH-DCM) to afford the product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-2-phenyl-8-vinylisoquinolin-1(2H)-one(8) as an off-while solid. ESI-MS m/z: 409.2 [M+H]⁺.

Example 6

Isoquinolinone 9 was prepared from compound 8 according to the followingprocedure:

A mixture of(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-2-phenyl-8-vinylisoquinolin-1(2H)-one(8) (120 mg, 0.29 mmol) and palladium (10% weight on carbon, 24 mg) inanhydrous MeOH (25 mL) was degassed and flushed with hydrogen (threecycles). The reaction mixture was stirred under a hydrogen atmosphere(hydrogen balloon) at RT for 1 h. The mixture was filtered throughCelite and rinsed with ethyl acetate. The filtrate was concentrated invacuo and the residue was purified by ISCO (silica gel cartridge, 0-10%MeOH-DCM) to afford the product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-8-ethyl-2-phenylisoquinolin-1(2H)-one(9). ESI-MS m/z: 411.2 [M+H]⁺.

Example 7

Isoquinoline 12 was prepared in 3 steps according to the followingprocedures. Amine 10 was prepared using Method I. The amine was thenconverted to 11 according to Method L followed by Method M. Compound 11was then converted to compound 12 in analogous fashion to compound 6 inExample 3. ESI-MS m/z: 413.2 [M+H]⁺.

Example 8

Isoquinolinone 13 was prepared from compound 11 in analogous fashion tocompound 12 in Example 7 except that pyridin-3-ylboronic acid was usedin place of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 424.2 [M+H]⁺.

Example 9

Isoquinoline 16 was prepared from compound 8 according to the followingprocedure:

To a solution of ethyl 2-(4-methyl-N-phenyl-2-vinylnicotinamido)acetate(8) (767 mg, 1.88 mmol) in 1,4-dioxane-H₂O (3:1, 20 mL) at RT, osmiumtetraoxide (2.5% wt in H₂O, 0.5 mL, 0.05 mmol) was added and theresulting mixture was stirred at RT for 30 min. To this mixture, sodiumperiodate (1.21 g, 5.53 mmol) was added and the resulting mixture wasstirred at RT for 30 h. The mixture was filtered through celite and thefiltrate was extracted with ethyl acetate (100 mL×2). The combinedorganic layer was washed with brine, dried over Na₂SO₄ and filtered. Thefiltrate was concentrated in vacuo to afford the product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-1-oxo-2-phenyl-1,2-dihydroisoquinoline-8-carbaldehyde(15) (730 mg, 95% yield) as a yellowish solid. ESI-MS m/z: 411.2 [M+H]⁺.

To a solution of(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-1-oxo-2-phenyl-1,2-dihydroisoquinoline-8-carbaldehyde(15) (50 mg, 0.12 mmol) in anhydrous 1-methyl-2-pyrrolidinone (3 mL),hydroxylamine hydrochloride (17 mg, 0.24 mmol) was added and theresulting mixture was stirred at 120° C. for 16 h. The mixture wasallowed to cool to RT, partitioned between ethyl acetate and water. Theorganic layer was washed with brine, dried over Na₂SO₄ and filtered. Thefiltrate was concentrated in vacuo and the residue was purified by ISCO(silica gel cartridge, 0-10% MeOH-DCM) to afford the product,(S)-3-(1-((9H-purin-6-yl)amino)ethyl)-1-oxo-2-phenyl-1,2-dihydroisoquinoline-8-carbonitrile(16) (14 mg, 28% yield) as a while solid. ESI-MS m/z: 408.2 [M+H]⁺.

Example 10

Isoquinolinone 17 was prepared in analogous fashion to compound 5 inExample 2 except that dimethylamine THF solution was used in place of1-methylpiperazine. ESI-MS m/z: 426.20 [M+H]⁺.

Example 11

Isoquinolinone 18 was prepared from compound 3 in analogous fashion tocompound 6 in Example 3 except that 1H-pyrazol-3-boronic acid was usedin place of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 449.2 [M+H]⁺.

Example 12

Isoquinolinone 19 was prepared from compound 3 in analogous fashion tocompound 6 in Example 3 except that (1-methyl-1H-pyrazol-4-yl)boronicacid was used in place of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 463.2[M+H]⁺.

Example 13

Isoquinolinone 20 was prepared from compound 11 in analogous fashion tocompound 12 in Example 7 except that (1-methyl-1H-pyrazol-4-yl)boronicacid was used in place of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 427.2[M+H]⁺.

Example 14

Isoquinolinone 21 was prepared from compound 3 in analogous fashion tocompound 6 in Example 3 except that pyridine-4-boronic acid was used inplace of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 458.2 [M+H]⁺.

Example 15

Isoquinolinone 25 was prepared from compound 3 in analogous fashion tocompound 6 in Example 3 except that (3-fluorophenyl)boronic acid wasused in place of 1H-pyrazole-4-boronic acid. ESI-MS m/z: 477.2 [M+H]⁺.

Example 16

Isoquinolinone 27 was prepared from compound 2 in 2 steps:

Compound 2 was converted to compound 26 according to the followingSuzuki coupling procedure.8-Chloro-2-phenyl-3-((S)-1-(9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-ylamino)ethyl)isoquinolin-1(2H)-one(2) (100 mg, 0.2 mmol, 1.0 eq), 6-methylpyridin-3-ylboronic acid (56 mg,0.41 mmol, 2.0 eq), Pd(OAc)₂ (9 mg, 0.04 mmol, 0.2 eq),2-(dicyclohexylphosphino)-2′,4′,6′-triisopropylbiphenyl (58 mg, 0.12mmol, 0.6 eq) and Na₂CO₃ (64 mg, 0.6 mmol, 3.0 eq) were dissolved in1-methyl-2-pyrrolidinone (10 mL). The resulting mixture was degassed andback-filled with argon three times, and then stirred at 160° C. under anargon atmosphere for 1.5 h. The reaction was complete based on TLCanalysis. The mixture was concentrated in vacuo and the residue waspurified by flash column chromatography on silica gel (1:30 MeOH-DCM) toafford the product,8-(6-methylpyridin-3-yl)-2-phenyl-3-((S)-1-(9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-ylamino)ethyl)isoquinolin-1(2H)-one(26); ESI-MS m/z: 558.30 [M+H]⁺.

Compound 26 was then converted to the product 27 using Method M. ESI-MSm/z: 474.20 [M+H]⁺.

Example 17

Isoquinolinone 29 was prepared from compound 2 in 2 steps:

Compound 2 first was converted to compound 28 using the followingBuchwald-Hartwig coupling procedure: A mixture of8-chloro-2-phenyl-3-((S)-1-(9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-ylamino)ethyl)isoquinolin-1(2H)-one(2) (300 mg, 0.6 mmol, 1.0 eq), pyrazole (61 mg, 0.9 mmol, 1.5 eq),L-proline (14 mg, 0.12 mmol, 0.2 eq), copper(I) iodide (12 mg, 0.06mmol, 0.1 eq), and potassium phosphate (318 mg, 1.5 mmol, 2.5 eq) wassuspended in DMSO (10 mL). The resulting mixture was degassed andback-filled with argon three times and stirred at 140° C. under an argonatmosphere overnight. After the reaction mixture was cooled to RT, itwas diluted with water (50 mL) and extracted with ethyl acetate (30mL×3). The combined organic layers were washed with brine (30 mL×2),dried over Na₂SO₄ and filtered. The filtrate was concentrated in vacuo.The resultant residue was purified by flash column chromatography onsilica gel (1% MeOH-DCM) to afford the product,2-phenyl-8-(1H-pyrazol-1-yl)-3-((S)-1-(9-(tetrahydro-2H-pyran-2-yl)-9H-purin-6-ylamino)ethyl)isoquinolin-1(2H)-one(28). ESI-MS m/z: 533.30 [M+H]⁺.

Compound 28 was then converted to compound 29 using Method M. ESI-MSm/z: 449.25 [M+H]⁺.

Example 18

Isoquinolinone 30 was prepared from compound 2 in analogous fashion tocompound 29 in Example 17 except that 4-methyl-1H-pyrazole was used inplace of 1H-pyrazole. ESI-MS m/z: 463.25 [M+H]⁺.

Example 19

Isoquinolinone 31 was prepared from compound 2 in analogous fashion tocompound 29 in Example 17 except that 4-methyl-1H-imidazole was used inplace of 1H-pyrazole. ESI-MS m/z: 463.20 [M+H]⁺.

Example 20

Isoquinolinone 33 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 32 using Method L (intermediate B-2 wasprepared by Method B). Compound 32 was then converted to 33 according tothe following procedure:

(S)-3-(1-(4-Amino-1,3,5-triazin-2-ylamino)ethyl)-8-chloro-2-phenylisoquinolin-1(2H)—one (32) (100 mg, 0.26 mmol, 1.0 eq),1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole(106 mg, 0.51 mmol, 2 eq), PdCl₂(dppf) (16 mg, 0.02 mmol, 0.08 eq), andNa₂CO₃ (81 mg, 0.765 mmol, 3.0 eq) were suspended in a mixture ofN,N-dimethylacetamide (20 mL) and water (1 mL). The resulting mixturewas degassed and back-filled with argon three times and stirred at 120°C. under an argon atmosphere for 16 h. The mixture was concentrated invacuo and the residue was purified by flash column chromatography onsilica gel (1-4% MeOH-DCM) to afford the product,3-((S)-1-(4-amino-1,3,5-triazin-2-ylamino)ethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(33). ESI-MS m/z: 439.25 [M+H]⁺.

Example 21

Isoquinolinone 34 was prepared from compound 32 in analogous fashion tocompound 33 in Example 20 except that 6-methylpyridin-3-ylboronic acidwas used in place of1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole.ESI-MS m/z: 450.25 [M+H]⁺.

Example 22

Isoquinolinone 36 was prepared from compound 1 in 3 steps. Compound 1was first converted to compound 35 using Method L. Compound 35 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous procedures for compound 33 in Example 20 after whichit was converted to compound 36 using Method M. ESI-MS m/z: 478.2[M+H]⁺.

Example 23

Isoquinolinone 37 was prepared from compound 35 in analogous fashion tocompound 36 in Example 22 except that 6-methylpyridin-3-ylboronic acidwas used in place of1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole.ESI-MS m/z: 487.2 [M−H]⁻.

Example 24

Isoquinolinone 38 was prepared from compound 35 in analogous fashion tocompound 36 in Example 22 except that pyridin-3-ylboronic acid was usedin place of1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole.ESI-MS m/z: 475.30 [M+H]⁺.

Example 25

Isoquinolinone 39 was prepared in analogous fashion to compound 4 inExample 1 except that morpholine was used in place of pyrrolidine.ESI-MS m/z: 468.0 [M+H]⁺.

Example 26

Isoquinolinone 40 was prepared in analogous fashion to compound 4 inExample 1 except that tetrahydro-2H-pyran-4-amine was used in place ofpyrrolidine. ESI-MS m/z: 482.2 [M+H]⁺.

Example 27

Isoquinolinone 41 was prepared from compound 2 in analogous fashion tocompound 27 in Example 16 except that 2-methylpyridin-4-ylboronic acidwas used in place of 6-methylpyridin-3-ylboronic acid. ESI-MS m/z:474.30 [M+H]⁺.

Example 28

Isoquinolinone 45 was prepared according to the following sequences:Amine 42 was prepared by Method I and converted to compound 43 usingMethod L. The compound 44 was then obtained in analogous fashion tocompound 27 in Example 16. Compound 44 was then converted to compound 45using Method M. ESI-MS m/z: 481.45 (M+H)⁺.

Example 29

Isoquinoline 49 was prepared according to the following sequences: Amine46 was prepared by Method I and converted to compound 47 using Method L.Compound 48 was then coupled to pyridin-3-ylboronic using the analogousprocedure in Example 20 after which it was converted to the compound 49according to the following procedure:

Compound 48 (290 mg, 0.49 mmol) was dissolved in trifluoroacetic acid(20 mL) and the resulting mixture was stirred at reflux for 48 h. Themixture was allowed to cool RT and then concentrated in vacuo to removethe excess amount of trifluoroacetic acid. The residue was diluted withwater (50 mL), neutralized with aqueous Na₂CO₃ solution to adjust the PHto 8 and then extracted with DCM (100 mL×3). The combined organic layerwas dried over anhydrous Na₂SO₄ and filtered. The filtrate wasconcentrated to dryness in vacuo and the residue was purified by flashchromatography on silica gel (gradient of 1-20% methanol/methylenechloride) to give the product 49 (80 mg, 42.6% yield) as an off-whitesolid. ESI-MS m/z: 384.2 [M+H]⁺.

Example 30

Compound 50 was prepared in analogous fashion to compound 49 in Example29 except that1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole wasused in place of 3-pyridylboronic acid. ESI-MS m/z: 387.2 [M+H]⁺.

Example 31

Isoquinolinone 52 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 51 using Method L. Compound 51 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 52.ESI-MS m/z: 463.4 [M+H]⁺.

Example 32

Isoquinolinone 54 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 53 using Method L. Compound 53 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 54.ESI-MS m/z: 463.35 [M+H]⁺.

Example 33

Isoquinolinone 56 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 55 using Method L. Compound 55 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 56.ESI-MS m/z: δ 487.2 [M+H]⁺.

Example 34

Isoquinolinone 58 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 57 using Method L. Compound 57 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 58.ESI-MS m/z: 505.2 [M+H]⁺.

Example 35

Isoquinolinone 60 was prepared from compound 1 in 2 steps. Compound 1was converted to compound 59 using Method L. Compound 59 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 60.ESI-MS m/z: 480.2 [M+H]⁺.

Example 36

Isoquinolinone 62 was prepared from compound 10 in 2 steps. Compound 10was converted to compound 61 using Method L. Compound 61 was thencoupled to1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazoleusing the analogous conditions from Example 20 to provide compound 62.ESI-MS m/z: 444.2 [M+H]⁺.

Example 37

To a mixture of(S)-3-(1-aminoethyl)-8-chloro-2-phenylisoquinolin-1(2H)-one (1) (1.0 g,3.35 mmol) and 1-methyl-1h-pyrazole-4-boronic acid (815 mg, 5.02 mmol)in anhydrous DMA (10 mL) in a sealed tube, PdCl₂(dppf) (219 mg, 0.27mmol) and aqueous Na₂CO₃ solution (1 M, 10.0 mL, 10.0 mmol) were addedand the resulting mixture was stirred at 120° C. for 3 h. The reactionmixture was allowed to cool to RT, quenched with water, and thenextracted with ethyl acetate (200 mL×3). The combined organic layerswere washed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo and the residue was purified by ISCO (silica gelcartridge, 0-8% MeOH-DCM) to afford the product,(S)-3-(1-aminoethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(63) (990 mg, 85% yield) as a pink/magenta solid. ESI-MS m/z: 345.2[M+H]⁺.

(S)-3-(1-Aminoethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(63) (570 mg, 1.66 mmol), 2,4-dichloro-5-iodopyrimidine (455 mg, 1.66mmol) and DIEA (0.27 mL, 1.66 mmol) were dissolved in n-butanol (12 mL)in a sealed tube, and the resulting mixture was stirred at 100° C. for16 h. The mixture was allowed to cool to RT, quenched with water andextracted with ethyl acetate (150 mL×2). The combined organic layerswere washed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo to afford the product(S)-3-(1-((2-chloro-5-iodopyrimidin-4-yl)amino)ethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(64) as an oil. The product obtained was used in the next step withoutpurification. ESI-MS m/z: 583.0 [M+H]⁺.

To a solution of(S)-3-(1-((2-chloro-5-iodopyrimidin-4-yl)amino)ethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(64) (964 mg, 1.65 mmol) in anhydrous 1,4-dioxane (5 mL) in a sealedtube, ammonium hydroxide (6 mL) was added and the resulting mixture wasstirred at 110° C. for 16 h. An additional amount of ammonium hydroxide(3 mL) was added to the reaction mixture and stirring was continued for16 h. The mixture was allowed to cool to RT, quenched with water andextracted with ethyl acetate (100 mL×2). The combined organic layerswere washed with brine, dried over Na₂SO₄ and filtered. The filtrate wasconcentrated in vacuo and the residue was purified by ISCO (silica gelcartridge, 0-8% MeOH-DCM) to afford the product,(S)-3-(1-((2-amino-5-iodopyrimidin-4-yl)amino)ethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(65) (532 mg, 57% yield) as a light tan solid. ESI-MS m/z: 564.0 [M+H]⁺.

Example 38

Compound 67 was prepared in 2 steps from amine 10. Compound 66 wasprepared using analogous Suzuki coupling procedures as in the conversionof 1 to 63 in Example 37. Compound 66 was then converted to 67 using thesame conditions in Example 37 except that H-2 was used in place of2,4-dichloro-5-iodopyrimidine. ESI-MS m/z: 470.2 [M+H]⁺.

Example 39

Compound 68 was prepared in analogous fashion to compound 64 in Example37 except that H-2 was used in place of 2,4-dichloro-5-iodopyrimidine.ESI-MS m/z: 506.2 [M+H]⁺.

Example 40

To a solution of(S)-3-(1-((2-amino-5-iodopyrimidin-4-yl)amino)ethyl)-8-(1-methyl-1H-pyrazol-4-yl)-2-phenylisoquinolin-1(2H)-one(65) (240 mg, 0.43 mmol) in anhydrous acetonitrile (12 mL) in a sealedtube, sodium cyanide (209 mg, 4.26 mmol), tetrakis(triphenylphosphine)palladium(0) (246 mg, 0.21 mmol), and copper iodide (57 mg, 0.30 mmol)were added and the resulting mixture was stirred at 80° C. for 16 h. Themixture was allowed to cool to RT, quenced with water and extracted withethyl acetate (50 mL×2). The combined organic layer was washed withbrine, dried over Na₂SO₄ and filtered. The filtrate was concentrated invacuo and the residue was purified by ISCO (silica gel cartridge, 0-10%MeOH-DCM) to afford the product,(S)-2-amino-4-((1-(8-(1-methyl-1H-pyrazol-4-yl)-1-oxo-2-phenyl-1,2-dihydroisoquinolin-3-yl)ethyl)amino)pyrimidine-5-carbonitrile(69) (60 mg, 30% yield). ESI-MS m/z: 463.2 [M+H]⁺.

Example 41

Compound 72 was prepared in 3 steps from compound 66. Compound 66 wasconverted to 70 and then 71 using the analogous procedures in Example37. Compound 71 was then converted to the product 72 using the procedurein Example 40. ESI-MS m/z: 427.2 [M+H]⁺.

Example 42

Compound 73 was prepared in two steps from compound 1 according to thefollowing procedures: Compound 1 (860 mg, 2.9 mmol, 1 eq.),1-methylpyrazole-4-boronic acid pinacol ester (1.8 g, 3 eq.), sodiumcarbonate (1.6 g, 5 eq.), palladium diacetate (100 mg, 0.15 eq.) andRuPhos (400 mg, 0.30 eq) were combined in a 20 mL septum-sealedmicrowave reaction tube with stir bar. The tube was purged with vacuumand refilled with dry argon three times, then charged with 1,4-dioxane(16 mL) and water (4 mL), and subjected to microwave heating at 125° C.for 3 h. The reaction mixture was then purified using flash silica gelchromatography (30 g of silica gel packed using a solution of 1%triethylamine in methylene chloride, mobile phase was a gradient of 1-4%methanol:methylene chloride) NMR analysis revealed this material to be amixture of the amine 63 and 2.6 eq. of pinacol; this mixture was takenforward without further purification.

A 15 mL thick-walled tube with o-ring seal and stir bar was charged withamine intermediate Z (53% by mass, 300 mg, 0.46 mmol, 1 eq.), n-butanol(5 mL), diisopropylethylamine (160 uL, 2 eq.), and4-chloro-5-cyano-6-aminopyrimidine (110 mg, 1.5 eq., commerciallyavailable from Ark Pharm, Inc.), capped tightly, and heated in a 120° C.bath during 3 d. The solvent was removed in vacuo, the residue taken upin DCM and treated with silica gel, and concentrated. The compound wasinitially purified using flash silica gel chromatography (gradient of0-5% methanol:methylene chloride). A sample of this material was furtherpurified by partitioning between diethyl ether and 5% acetic acid inwater, discarding the ether layer, and extracting the aqueous threetimes with methylene chloride. The combine organic layers were driedover sodium sulfate to provide compound 73 in 31% yield. ESI-MS m/z:463.26 [M+H]+.

Example 43

Compound 74 was prepared in analogous fashion to compound 72 in Example41 except that 2,4,5-trichloropyrimidine was used in place of2,4-dichloro-5-iodopyrimidine. ESI-MS m/z: 472.2 [M+H]⁺.

Example 44

Compound 76 was prepared from compound 2 in two steps: A 2 mLthick-walled microwave-reaction tube with stir bar was charged withcompound 2 (120 mg, 0.24 mmol, 1 eq.), 2-methoxypyrimidine-5-boronicacid (74 mg, 2 eq.), sodium carbonate (130 mg, 5 eq.), palladiumdiacetate (8 mg, 0.15 eq.) and RuPhos (34 mg, 0.30 eq.), then cappedwith a septum and purged three time with vacuum, refilling with dryargon. 1,4-Dioxane (1.6 mL) and water (0.4 mL) were added and thereaction subjected to microwave heating at 125° C. during 3 h, at whichtime LC/MS showed complete consumption of the starting chloride. Thereaction mixture was diluted with DCM, treated with silica gel (0.5 g)and concentrated, then purified by flash chromatography, eluting 15 gsilica gel (gradient 1-4% methanol/methylene chloride) to provide 140 mgof compound 75 as an off-white powder. ESI-MS m/z 575.36 [M+H]+.

Compound 75 was then converted to compound 76 using Method M. ESI-MSm/z: 491.22 [M+H]+.

Example 45

Compound 77 was prepared in analogous fashion to compound 75 in Example44 except that 2-methylpyrimidin-5-ylboronic acid was used in place of2-methoxypyrimidin-5-ylboronic acid. ESI-MS m/z 475.21 [M+H]+

Example 46

Compound 78 was prepared in analogous fashion to compound 64 in Example37 except that N-5 was used in place of 2,4-dichloro-5-iodopyrimidineand isopropanol was used in place of n-butanol. ESI-MS m/z: 506.2[M+H]+.

Example 47

Compound 79 was prepared from 69 according to the following procedure:

To a solution of(S)-2-amino-4-((1-(8-(1-methyl-1H-pyrazol-4-yl)-1-oxo-2-phenyl-1,2-dihydroisoquinolin-3-yl)ethyl)amino)pyrimidine-5-carbonitrile(69) (30.4 mg, 0.066 mmol) in anhydrous toluene (1 mL), acetaldoxime (10μL, 0.13 mmol), palladium acetate (2 mg, 0.0066 mmol) and triphenylphosphine (4 mg, 0.013 mmol) were added and the resulting mixture wasstirred at 80° C. for 2 h. Additional amounts of acetaldoxime (10 μL,0.13 mmol), palladium acetate (2 mg, 0.0066 mmol) and triphenylphosphine (4 mg, 0.013 mmol) were added and stirring was continued at80° C. for 2 h. The mixture was allowed to cool to RT, quenched withwater (30 mL), and then extracted with ethyl acetate (30 mL×2). Thecombined organic layers were washed with brine, dried over Na₂SO₄ andfiltered. The filtrate was concentrated in vacuo and the residue waspurified by ISCO column chromatography (silica gel cartridge, 0-8.5%MeOH-DCM) to afford the desired product,(S)-2-amino-4-((1-(8-(1-methyl-1H-pyrazol-4-yl)-1-oxo-2-phenyl-1,2-dihydroisoquinolin-3-yl)ethyl)amino)pyrimidine-5-carboxamide(79) as a white solid. ESI-MS m/z: 481.2 [M+H]+.

TABLE 4 In Vitro IC₅₀ data for selected compounds. + (greater than ++(less than +++ (less than ++++ (less than IC₅₀ (nM) 10 microMolar) 10microMolar) 1 microMolar 100 nM) PI3K δ Compound No. Compound No.Compound No. Compound No. 4, 17, 50, 54, 5, 29, 30, 34, 39, 40 6, 7, 9,12, 13, 16, 18, 19, 20, 21, 8, 25, 27, 31, 33, 36, 37, 38, 56, 41, 58,45, 49, 52, 62, 67, 68, 65, 69, 72, 73, 74, 76 PI3K γ Compound No.Compound No. Compound No. Compound No. 5, 50, 54 4, 17, 29, 30, 31, 33,6, 20, 39, 49, 52, 62, 7, 9, 12, 13, 16, 18, 34, 40, 76 74 19, 21, 8,25, 27, 36, 37, 38, 56, 41, 58, 45, 67, 68, 65, 69, 72, 73 PI3K αCompound No. Compound No. Compound No. Compound No. 4, 5, 16, 17, 18,19, 6, 7, 9, 13, 20, 21, 8, 12, 349, 36, 37, 38, 29, 30, 31, 33, 34, 39,25, 27, 58, 45, 52, 62, 56, 41 40, 49, 50, 54, 67, 68, 72, 73, 76 65,69, 74 PI3K β Compound No. Compound No. Compound No. Compound No. 4, 5,6, 17, 18, 19, 27, 7, 9, 16, 20, 21, 8, 25, 12, 13, 349 72 29, 30, 31,33, 34, 39, 36, 37, 38, 56, 41, 58, 40, 45, 49, 52, 50, 54, 62 67, 68,65, 69, 73, 74, 76 B cell Compound No. Compound No. Compound No.Compound No. proliferation 4, 29, 30, 34 5, 6, 7, 9, 12, 13, 16, EC₅₀(nM) 17, 18, 19, 20, 21, 8, 25, 27, 31, 33, 36, 37, 56, 41, 45, 49, 52,62, 67, 68

TABLE 5 Structures of the Compounds for the IC₅₀ results described inTable 4. Structure

Compound 4

Compound 5

Compound 6

Compound 7

Compound 9

Compound 12

Compound 13

Compound 16

Compound 17

Compound 18

Compound 19

Compound 20

Compound 21

Compound 8

Compound 25

Compound 27

Compound 29

Compound 30

Compound 31

Compound 33

Compound 34

Compound 36

Compound 37

Compound 38

Compound 56

Compound 39

Compound 40

Compound 41

Compound 58

Compound 45

Compound 49

Compound 52

Compound 50

Compound 54

Compound 60

Compound 62

Compound 67

Compound 68

Compound 65

Compound 69

Compound 73

Compound 72

Compound 74

Compound 76

Example 48 Expression and Inhibition Assays of p110α/p85α, p110β/p85α,p110δ/p85α, and p110γ

Class I PI3-Ks can be either purchased (p110α/p85α, p110β/p85α,p110β/p85α from Upstate, and p110γ from Sigma) or expressed aspreviously described (Knight et al., 2004). IC₅₀ values are measuredusing either a standard TLC assay for lipid kinase activity (describedbelow) or a high-throughput membrane capture assay. Kinase reactions areperformed by preparing a reaction mixture containing kinase, inhibitor(2% DMSO final concentration), buffer (25 mM HEPES, pH 7.4, 10 mMMgCl2), and freshly sonicated phosphatidylinositol (100 μg/ml).Reactions are initiated by the addition of ATP containing 10 μCi ofγ-32P-ATP to a final concentration of 10 or 100 μM and allowed toproceed for 5 minutes at room temperature. For TLC analysis, reactionsare then terminated by the addition of 105 μl 1N HCl followed by 160 μlCHCl₃:MeOH (1:1). The biphasic mixture is vortexed, briefly centrifuged,and the organic phase is transferred to a new tube using a gel loadingpipette tip precoated with CHCl₃. This extract is spotted on TLC platesand developed for 3-4 hours in a 65:35 solution of n-propanol:1M aceticacid. The TLC plates are then dried, exposed to a phosphorimager screen(Storm, Amersham), and quantitated. For each compound, kinase activityis measured at 10-12 inhibitor concentrations representing two-folddilutions from the highest concentration tested (typically, 200 μM). Forcompounds showing significant activity, IC₅₀ determinations are repeatedtwo to four times, and the reported value is the average of theseindependent measurements.

Other commercial kits or systems for assaying PI3-K activities areavailable. The commercially available kits or systems can be used toscreen for inhibitors and/or agonists of PI3-Ks including, but notlimited to, PI 3-Kinase α, β, δ, and γ. An exemplary system is PI3-Kinase (human) HTRF™ Assay from Upstate. The assay can be carried outaccording to the procedures suggested by the manufacturer. Briefly, theassay is a time resolved FRET assay that indirectly measures PIP3product formed by the activity of a PI3-K. The kinase reaction isperformed in a microtiter plate (e.g., a 384 well microtiter plate). Thetotal reaction volume is approximately 20 μl per well. In the firststep, each well receives 2 μl of test compound in 20% dimethylsulphoxideresulting in a 2% DMSO final concentration. Next, approximately 14.5 μlof a kinase/PIP2 mixture (diluted in 1× reaction buffer) is added perwell for a final concentration of 0.25-0.3 μg/ml kinase and 10 μM PIP2.The plate is sealed and incubated for 15 minutes at room temperature. Tostart the reaction, 3.5 μl of ATP (diluted in 1× reaction buffer) isadded per well for a final concentration of 10 μM ATP. The plate issealed and incubated for 1 hour at room temperature. The reaction isstopped by adding 5 μl of Stop Solution per well and then 5 μl ofDetection Mix is added per well. The plate is sealed, incubated for 1hour at room temperature, and then read on an appropriate plate reader.Data is analyzed and IC₅₀s are generated using GraphPad Prism 5.

Example 49 Expression and Inhibition Assays of Abl

The cross-activity or lack thereof of one or more compounds as disclosedherein against Abl kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be assayed in triplicate against recombinant full-length Ablor Abl (T315I) (Upstate) in an assay containing 25 mM HEPES, pH 7.4, 10mM MgCl₂, 200 μM ATP (2.5 μCi of γ-32P-ATP), and 0.5 mg/mL BSA. Theoptimized Abl peptide substrate EAIYAAPFAKKK is used as phosphoacceptor(200 μM). Reactions are terminated by spotting onto phosphocellulosesheets, which are washed with 0.5% phosphoric acid (approximately 6times, 5-10 minutes each). Sheets are dried and the transferredradioactivity quantitated by phosphorimaging.

Example 50 Expression and Inhibition Assays of Hck

The cross-activity or lack thereof of one or more compounds as disclosedherein against Hck kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be assayed in triplicate against recombinant full-length Hckin an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂, 200 μM ATP (2.5μCi of γ-32P-ATP), and 0.5 mg/mL BSA. The optimized Src family kinasepeptide substrate EIYGEFKKK is used as phosphoacceptor (200 μM).Reactions are terminated by spotting onto phosphocellulose sheets, whichare washed with 0.5% phosphoric acid (approximately 6 times, 5-10minutes each). Sheets are dried and the transferred radioactivityquantitated by phosphorimaging.

Example 51 Expression and Inhibition Assays of Inulsin Receptor (IR)

The cross-activity or lack thereof of one or more compounds as disclosedherein against IR receptor kinase can be measured according to anyprocedures known in the art or methods disclosed below. The compoundsdescribed herein can be assayed in triplicate against recombinantinsulin receptor kinase domain (Upstate) in an assay containing 25 mMHEPES, pH 7.4, 10 mM MgCl₂, 10 mM MnCl₂, 200 μM ATP (2.5 μCi ofγ-32P-ATP), and 0.5 mg/mL BSA. Poly E-Y (Sigma; 2 mg/mL) is used as asubstrate. Reactions are terminated by spotting onto nitrocellulose,which is washed with 1M NaCl/1% phosphoric acid (approximately 6 times,5-10 minutes each). Sheets are dried and the transferred radioactivityquantitated by phosphorimaging.

Example 52 Expression and Inhibition Assays of Src

The cross-activity or lack thereof of one or more compounds as disclosedherein against Src kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be assayed in triplicate against recombinant full-length Srcor Src (T338I) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,200 μM ATP (2.5 μCi of γ-32P-ATP), and 0.5 mg/mL BSA. The optimized Srcfamily kinase peptide substrate EIYGEFKKK is used as phosphoacceptor(200 μM). Reactions are terminated by spotting onto phosphocellulosesheets, which are washed with 0.5% phosphoric acid (approximately 6times, 5-10 minutes each). Sheets were dried and the transferredradioactivity quantitated by phosphorimaging.

Example 53 Expression and Inhibition Assays of DNA-PK (DNAK)

The cross-activity or lack thereof of one or more compounds as disclosedherein against DNAK kinase can be measured according to any proceduresknown in the art. DNA-PK can be purchased from Promega and assayed usingthe DNA-PK Assay System (Promega) according to the manufacturer'sinstructions.

Example 54 Expression and Inhibition Assays mTOR

The cross-activity or lack thereof of one or more compounds as disclosedherein against mTor can be measured according to any procedures known inthe art or methods disclosed below. The compounds described herein canbe tested against recombinant mTOR (Invitrogen) in an assay containing50 mM HEPES, pH 7.5, 1 mM EGTA, 10 mM MgCl₂, 2.5 mM, 0.01% Tween, 10 μMATP (2.5 μCi of γ-32P-ATP), and 3 μg/mL BSA. Rat recombinantPHAS-1/4EBP1 (Calbiochem; 2 mg/mL) is used as a substrate. Reactions areterminated by spotting onto nitrocellulose, which is washed with 1MNaCl/1% phosphoric acid (approximately 6 times, 5-10 minutes each).Sheets are dried and the transferred radioactivity quantitated byphosphorimaging.

Other kits or systems for assaying mTOR activity are commerciallyavailable. For instance, one can use Invitrogen's LanthaScreen™ Kinaseassay to test the inhibitors of mTOR disclosed herein. This assay is atime resolved FRET platform that measures the phosphorylation of GFPlabeled 4EBP1 by mTOR kinase. The kinase reaction is performed in awhite 384 well microtiter plate. The total reaction volume is 20 μl perwell and the reaction buffer composition is 50 mM HEPES pH 7.5, 0.01%Polysorbate 20, 1 mM EGTA, 10 mM MnCl₂, and 2 mM DTT. In the first step,each well receives 2 μl of test compound in 20% dimethylsulphoxideresulting in a 2% DMSO final concentration. Next, 8 μl of mTOR dilutedin reaction buffer is added per well for a 60 ng/ml final concentration.To start the reaction, 10 μl of an ATP/GFP-4EBP1 mixture (diluted inreaction buffer) is added per well for a final concentration of 10 μMATP and 0.5 μM GFP-4EBP1. The plate is sealed and incubated for 1 hourat room temperature. The reaction is stopped by adding 10 μl per well ofa Tb-anti-pT46 4EBP1 antibody/EDTA mixture (diluted in TR-FRET buffer)for a final concentration of 1.3 nM antibody and 6.7 mM EDTA. The plateis sealed, incubated for 1 hour at room temperature, and then read on aplate reader set up for LanthaScreen™ TR-FRET. Data is analyzed andIC₅₀s are generated using GraphPad Prism 5.

Example 55 Expression and Inhibition Assays of Vascular EndothelialGrowth Receptor

The cross-activity or lack thereof of one or more compounds as disclosedherein against VEGF receptor can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant KDR receptor kinase domain(Invitrogen) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,0.1% BME, 10 μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. Poly E-Y(Sigma; 2 mg/mL) is used as a substrate. Reactions are terminated byspotting onto nitrocellulose, which is washed with 1M NaCl/1% phosphoricacid (approximately 6 times, 5-10 minutes each). Sheets are dried andthe transferred radioactivity quantitated by phosphorimaging.

Example 56 Expression and Inhibition Assays of Ephrin Receptor B4(EphB4)

The cross-activity or lack thereof of one or more compounds as disclosedherein against EphB4 can be measured according to any procedures knownin the art or methods disclosed below. The compounds described hereincan be tested against recombinant Ephrin receptor B4 kinase domain(Invitrogen) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,0.1% BME, 10 μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. Poly E-Y(Sigma; 2 mg/mL) is used as a substrate. Reactions are terminated byspotting onto nitrocellulose, which is washed with 1M NaCl/1% phosphoricacid (approximately 6 times, 5-10 minutes each). Sheets are dried andthe transferred radioactivity quantitated by phosphorimaging.

Example 57 Expression and Inhibition Assays of Epidermal Growth FactorReceptor (EGFR)

The cross-activity or lack thereof of one or more compounds as disclosedherein against EGFR kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant EGF receptor kinase domain(Invitrogen) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,0.1% BME, 10 μM ATP (2.5 μCi of γ-32P-ATP), and 3 μg/mL BSA. Poly E-Y(Sigma; 2 mg/mL) is used as a substrate. Reactions are terminated byspotting onto nitrocellulose, which is washed with 1M NaCl/1% phosphoricacid (approximately 6 times, 5-10 minutes each). Sheets are dried andthe transferred radioactivity quantitated by phosphorimaging.

Example 58 Expression and Inhibition Assays of KIT Assay

The cross-activity or lack thereof of one or more compounds as disclosedherein against KIT kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant KIT kinase domain (Invitrogen)in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂, 1 mM DTT, 10 mMMnCl₂, 10 μM ATP (2.5 μCi of γ-32P-ATP), and 3 μg/mL BSA. Poly E-Y(Sigma; 2 mg/mL) is used as a substrate. Reactions are terminated byspotting onto nitrocellulose, which is washed with 1M NaCl/1% phosphoricacid (approximately 6 times, 5-10 minutes each). Sheets are dried andthe transferred radioactivity quantitated by phosphorimaging.

Example 59 Expression and Inhibition Assays of RET

The cross-activity or lack thereof of one or more compounds as disclosedherein against RET kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant RET kinase domain (Invitrogen)in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂, 2.5 mM DTT, 10μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. The optimized Ablpeptide substrate EAIYAAPFAKKK is used as phosphoacceptor (200 μM).Reactions are terminated by spotting onto phosphocellulose sheets, whichare washed with 0.5% phosphoric acid (approximately 6 times, 5-10minutes each). Sheets are dried and the transferred radioactivityquantitated by phosphorimaging.

Example 60 Expression and Inhibition Assays of Platelet Derived GrowthFactor Receptor (PDGFR)

The cross-activity or lack thereof of one or more compounds as disclosedherein against PDGFR kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant PDG receptor kinase domain(Invitrogen) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,2.5 mM DTT, 10 μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. Theoptimized Abl peptide substrate EAIYAAPFAKKK is used as phosphoacceptor(200 μM). Reactions are terminated by spotting onto phosphocellulosesheets, which are washed with 0.5% phosphoric acid (approximately 6times, 5-10 minutes each). Sheets are dried and the transferredradioactivity quantitated by phosphorimaging.

Example 61 Expression and Inhibition Assays of FMS-Related TyrosineKinase 3 (FLT-3)

The cross-activity or lack thereof of one or more compounds as disclosedherein against FLT-3 kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant FLT-3 kinase domain(Invitrogen) in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂,2.5 mM DTT, 10 μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. Theoptimized Abl peptide substrate EAIYAAPFAKKK is used as phosphoacceptor(200 μM). Reactions are terminated by spotting onto phosphocellulosesheets, which are washed with 0.5% phosphoric acid (approximately 6times, 5-10 minutes each). Sheets are dried and the transferredradioactivity quantitated by phosphorimaging.

Example 62 Expression and Inhibition Assays of TEK Receptor TyrosineKinase (TIE2)

The cross-activity or lack thereof of one or more compounds as disclosedherein against TIE2 kinase can be measured according to any proceduresknown in the art or methods disclosed below. The compounds describedherein can be tested against recombinant TIE2 kinase domain (Invitrogen)in an assay containing 25 mM HEPES, pH 7.4, 10 mM MgCl₂, 2 mM DTT, 10 mMMnCl₂, 10 μM ATP (2.5 μCi of μ-32P-ATP), and 3 μg/mL BSA. Poly E-Y(Sigma; 2 mg/mL) is used as a substrate. Reactions are terminated byspotting onto nitrocellulose, which is washed with 1M NaCl/1% phosphoricacid (approximately 6 times, 5-10 minutes each). Sheets are dried andthe transferred radioactivity quantitated by phosphorimaging.

Example 63 B Cell Activation and Proliferation Assay

The ability of one or more subject compounds to inhibit B cellactivitation and proliferation is determined according to standardprocedures known in the art. For example, an in vitro cellularproliferation assay is established that measures the metabolic activityof live cells. The assay is performed in a 96 well microtiter plateusing Alamar Blue reduction. Balb/c splenic B cells are purified over aFicoll-Paque™ PLUS gradient followed by magnetic cell separation using aMACS B cell Isolation Kit (Miletenyi). Cells are plated in 90 μl at50,000 cells/well in B Cell Media (RPMI+10% FBS+Penn/Strep+50 μM bME+5mM HEPES). A compound disclosed herein is diluted in B Cell Media andadded in a 10 μl volume. Plates are incubated for 30 min at 37° C. and5% CO₂ (0.2% DMSO final concentration). A 50 μl B cell stimulationcocktail is then added containing either 10 μg/ml LPS or 5 μg/ml F(ab′)2Donkey anti-mouse IgM plus 2 ng/ml recombinant mouse IL4 in B CellMedia. Plates are incubated for 72 hours at 37° C. and 5% CO₂. A volumeof 15 μL of Alamar Blue reagent is added to each well and plates areincubated for 5 hours at 37° C. and 5% CO₂. Alamar Blue fluoresce isread at 560Ex/590Em, and IC₅₀ or EC₅₀ values are calculated usingGraphPad Prism 5.

Example 64 Tumor Cell Line Proliferation Assay

The ability of one or more subject compounds to inhibit tumor cell lineproliferation can be determined according to standard procedures knownin the art. For instance, an in vitro cellular proliferation assay canbe performed to measure the metabolic activity of live cells. The assayis performed in a 96 well microtiter plate using Alamar Blue reduction.Human tumor cell lines are obtained from ATCC (e.g., MCF7, U-87 MG,MDA-MB-468, PC-3), grown to confluency in T75 flasks, trypsinized with0.25% trypsin, washed one time with Tumor Cell Media (DMEM+10% FBS), andplated in 90 μl at 5,000 cells/well in Tumor Cell Media. A compounddisclosed herein is diluted in Tumor Cell Media and added in a 10 ulvolume. Plates are incubated for 72 hours at 37° C. and 5% CO₂. A volumeof 10 μL of Alamar Blue reagent is added to each well and plates areincubated for 3 hours at 37° C. and 5% CO₂. Alamar Blue fluoresce isread at 560Ex/590Em, and IC₅₀ values are calculated using GraphPad Prism5.

Example 65 Antitumor Activity In Vivo

The compounds described herein can be evaluated in a panel of human andmurine tumor models.

Paclitaxel-Refractory Tumor Models

1. Clinically-Derived Ovarian Carcinoma Model.

This tumor model is established from a tumor biopsy of an ovarian cancerpatient. Tumor biopsy is taken from the patient. The compounds describedherein are administered to nude mice bearing staged tumors using anevery 2 days×5 schedule.

2. A2780Tax Human Ovarian Carcinoma Xenograft (Mutated Tubulin).

A2780Tax is a paclitaxel-resistant human ovarian carcinoma model. It isderived from the sensitive parent A2780 line by co-incubation of cellswith paclitaxel and verapamil, an MDR-reversal agent. Its resistancemechanism has been shown to be non-MDR related and is attributed to amutation in the gene encoding the beta-tubulin protein. The compoundsdescribed herein can be administered to mice bearing staged tumors on anevery 2 days×5 schedule.

3. HCT116/VM46 Human Colon Carcinoma Xenograft (Multi-Drug Resistant).

HCT116/VM46 is an MDR-resistant colon carcinoma developed from thesensitive HCT116 parent line. In vivo, grown in nude mice, HCT116/VM46has consistently demonstrated high resistance to paclitaxel. Thecompounds described herein can be administered to mice bearing stagedtumors on an every 2 days×5 schedule.

4. M5076 Murine Sarcoma Model

M5076 is a mouse fibrosarcoma that is inherently refractory topaclitaxel in vivo. The compounds described herein can be administeredto mice bearing staged tumors on an every 2 days×5 schedule.

One or more compounds as disclosed herein can be used in combinationother therapeutic agents in vivo in the multidrug resistant human coloncarcinoma xenografts HCT/VM46 or any other model known in the artincluding those described herein.

Example 66 Microsome Stability Assay

The stability of one or more subject compounds is determined accordingto standard procedures known in the art. For example, stability of oneor more subject compounds is established by an in vitro assay. Forexample, an in vitro microsome stability assay is established thatmeasures stability of one or more subject compounds when reacting withmouse, rat or human microsomes from liver. The microsome reaction withcompounds is performed in 1.5 mL Eppendorf tube. Each tube contains 0.1μL of 10.0 mg/ml NADPH; 75 μL of 20.0 mg/ml mouse, rat or human livermicrosome; 0.4 μL of 0.2 M phosphate buffer, and 425 μL of ddH₂O.Negative control (without NADPH) tube contains 75 μL of 20.0 mg/mlmouse, rat or human liver microsome; 0.4 μL of 0.2 M phosphate buffer,and 525 μL of ddH₂O. The reaction is started by adding 1.0 μL of 10.0 mMtested compound. The reaction tubes are incubated at 37° C. 100 μLsample is collected into new Eppendorf tube containing 300 μL coldmethanol at 0, 5, 10, 15, 30 and 60 minutes of reaction. Samples arecentrifuged at 15,000 rpm to remove protein. Supernatant of centrifugedsample is transferred to new tube. Concentration of stable compoundafter reaction with microsome in the supernatant is measured by LiquidChromatography/Mass Spectrometry (LC-MS).

Example 67 Plasma Stability Assay

The stability of one or more subject compounds in plasma is determinedaccording to standard procedures known in the art. See, e.g., RapidCommun. Mass Spectrom., 10: 1019-1026. The following procedure is anHPLC-MS/MS assay using human plasma; other species including monkey,dog, rat, and mouse are also available. Frozen, heparinized human plasmais thawed in a cold water bath and spun for 10 minutes at 2000 rpm at 4°C. prior to use. A subject compound is added from a 400 μM stocksolution to an aliquot of pre-warmed plasma to give a final assay volumeof 400 μL (or 800 μL for half-life determination), containing 5 μM testcompound and 0.5% DMSO. Reactions are incubated, with shaking, for 0minutes and 60 minutes at 37° C., or for 0, 15, 30, 45 and 60 minutes at37 C for half life determination. Reactions are stopped by transferring50 μL of the incubation mixture to 200 μL of ice-cold acetonitrile andmixed by shaking for 5 minutes. The samples are centrifuged at 6000×gfor 15 minutes at 4° C. and 120 μL of supernatant removed into cleantubes. The samples are then evaporated to dryness and submitted foranalysis by HPLC-MS/MS.

In one embodiment, one or more control or reference compounds (5 μM) aretested simultaneously with the test compounds: one compound,propoxycaine, with low plasma stability and another compound,propantheline, with intermediate plasma stability.

Samples are reconstituted in acetonitrile/methanol/water (1/1/2, v/v/v)and analyzed via (RP)HPLC-MS/MS using selected reaction monitoring(SRM). The HPLC conditions consist of a binary LC pump with autosampler,a mixed-mode, C12, 2×20 mm column, and a gradient program. Peak areascorresponding to the analytes are recorded by HPLC-MS/MS. The ratio ofthe parent compound remaining after 60 minutes relative to the amountremaining at time zero, expressed as percent, is reported as plasmastability. In case of half-life determination, the half-life isestimated from the slope of the initial linear range of the logarithmiccurve of compound remaining (%) vs. time, assuming first order kinetics.

Example 68 Chemical Stability

The chemical stability of one or more subject compounds is determinedaccording to standard procedures known in the art. The following detailsan exemplary procedure for ascertaining chemical stability of a subjectcompound. The default buffer used for the chemical stability assay isphosphate-buffered saline (PBS) at pH 7.4; other suitable buffers can beused. A subject compound is added from a 100 μM stock solution to analiquot of PBS (in duplicate) to give a final assay volume of 400 μL,containing 5 μM test compound and 1% DMSO (for half-life determination atotal sample volume of 700 μL is prepared). Reactions are incubated,with shaking, for 24 hours at 37° C.; for half-life determinationsamples are incubated for 0, 2, 4, 6, and 24 hours. Reactions arestopped by adding immediately 100 μL of the incubation mixture to 100 μLof acetonitrile and vortexing for 5 minutes. The samples are then storedat −20° C. until analysis by HPLC-MS/MS. Where desired, a controlcompound or a reference compound such as chlorambucil (5 μM) is testedsimultaneously with a subject compound of interest, as this compound islargely hydrolyzed over the course of 24 hours. Samples are analyzed via(RP)HPLC-MS/MS using selected reaction monitoring (SRM). The HPLCconditions consist of a binary LC pump with autosampler, a mixed-mode,C12, 2×20 mm column, and a gradient program. Peak areas corresponding tothe analytes are recorded by HPLC-MS/MS. The ratio of the parentcompound remaining after 24 hours relative to the amount remaining attime zero, expressed as percent, is reported as chemical stability. Incase of half-life determination, the half-life is estimated from theslope of the initial linear range of the logarithmic curve of compoundremaining (%) vs. time, assuming first order kinetics.

Example 69 Akt Kinase Assay

Cells comprising components of the Akt/mTOR pathway, including but notlimited to L6 myoblasts, B-ALL cells, B-cells, T-cells, leukemia cells,bone marrow cells, p190 transduced cells, philladelphia chromosomepositive cells (Ph+), and mouse embryonic fibroblasts, are typicallygrown in cell growth media such as DMEM supplemented with fetal bovineserum and/or antibiotics, and grown to confluency.

In order to compare the effect of one or more compounds disclosed hereinon Akt activation, said cells are serum starved overnight and incubatedwith one or more compounds disclosed herein or about 0.1% DMSO forapproximately 1 minute to about 1 hour prior to stimulation with insulin(e.g., 100 nM) for about 1 minute to about 1 hour. Cells are lysed byscraping into ice cold lysis buffer containing detergents such as sodiumdodecyl sulfate and protease inhibitors (e.g., PMSF). After contactingcells with lysis buffer, the solution is briefly sonicated, cleared bycentrifugation, resolved by SDS-PAGE, transferred to nitrocellulose orPVDF and immunoblotted using antibodies to phospho-Akt S473, phospho-AktT308, Akt, and β-actin (Cell Signaling Technologies).

The results demonstrate that one or more compounds of the presentdisclosure inhibit insulin stimulated phosphorylation of Akt at S473.Alternatively, some compounds disclosed herein additionally inhibitinsulin stimulated phosphorylation of Akt at T308. Such class ofcompounds can inhibit Akt more effectively than rapamycin and can beindicative of mTORC2 inhibitors or inhibitors of upstream kinases suchas PI3K or Akt.

Example 70 Kinase Signaling in Blood

PI3K/Akt/mTor signaling is measured in blood cells using the phosflowmethod (Methods Enzymol. (2007) 434:131-54). This method is by nature asingle cell assay so that cellular heterogeneity can be detected ratherthan population averages. This allows concurrent distinction ofsignaling states in different populations defined by other markers.Phosflow is also highly quantitative. To test the effects of one or morecompounds disclosed herein, unfractionated splenocytes, or peripheralblood mononuclear cells are stimulated with anti-CD3 to initiate T-cellreceptor signaling. The cells are then fixed and stained for surfacemarkers and intracellular phosphoproteins Inhibitors disclosed hereininhibit anti-CD3 mediated phosphorylation of Akt-S473 and S6, whereasrapamycin inhibits S6 phosphorylation and enhances Akt phosphorylationunder the conditions tested.

Similarly, aliquots of whole blood are incubated for 15 minutes withvehicle (e.g., 0.1% DMSO) or kinase inhibitors at variousconcentrations, before addition of stimuli to crosslink the T cellreceptor (TCR) (anti-CD3 with secondary antibody) or the B cell receptor(BCR) using anti-kappa light chain antibody (Fab′2 fragments). Afterapproximately 5 and 15 minutes, samples are fixed (e.g., with cold 4%paraformaldehyde) and used for phosflow. Surface staining is used todistinguish T and B cells using antibodies directed to cell surfacemarkers that are known to the art. The level of phosphorylation ofkinase substrates such as Akt and S6 are then measured by incubating thefixed cells with labeled antibodies specific to the phosphorylatedisoforms of these proteins. The population of cells are then analyzed byflow cytometry.

Example 71 Colony Formation Assay

Murine bone marrow cells freshly transformed with a p190 BCR-Ablretrovirus (herein referred to as p190 transduced cells) are plated inthe presence of various drug combinations in M3630 methylcellulose mediafor about 7 days with recombinant human IL-7 in about 30% serum, and thenumber of colonies formed is counted by visual examination under amicroscope.

Alternatively, human peripheral blood mononuclear cells are obtainedfrom Philadelphia chromosome positive (Ph+) and negative (Ph−) patientsupon initial diagnosis or relapse. Live cells are isolated and enrichedfor CD19+ CD34+ B cell progenitors. After overnight liquid culture,cells are plated in methocult GF+H4435, Stem Cell Technologies)supplemented with cytokines (IL-3, IL-6, IL-7, G-CSF, GM-CSF, CF, Flt3ligand, and erythropoietin) and various concentrations of knownchemotherapeutic agents in combination with either compounds of thepresent disclosure. Colonies are counted by microscopy 12-14 days later.This method can be used to test for evidence of additive or synergisticactivity.

Example 72 In Vivo Effect of Kinase Inhibitors on Leukemic Cells

Female recipient mice are lethally irradiated from a γ source in twodoses about 4 hr apart, with approximately 5 Gy each. About 1 hr afterthe second radiation dose, mice are injected i.v. with about 1×10⁶leukemic cells (e.g., Ph+ human or murine cells, or p190 transduced bonemarrow cells). These cells are administered together with aradioprotective dose of about 5×10⁶ normal bone marrow cells from 3-5week old donor mice. Recipients are given antibiotics in the water andmonitored daily. Mice who become sick after about 14 days are euthanizedand lymphoid organs are harvested for analysis. Kinase inhibitortreatment begins about 10 days after leukemic cell injection andcontinues daily until the mice become sick or a maximum of approximately35 days post-transplant. Inhibitors are given by oral lavage.

Peripheral blood cells are collected approximately on day 10(pre-treatment) and upon euthanization (post treatment), contacted withlabeled anti-hCD4 antibodies and counted by flow cytometry. This methodcan be used to demonstrate that the synergistic effect of one or morecompounds disclosed herein in combination with known chemotherapeuticagents can reduce leukemic blood cell counts as compared to treatmentwith known chemotherapeutic agents (e.g., Gleevec) alone under theconditions tested.

Example 73 Treatment of Lupus Disease Model Mice

Mice lacking the inhibitory receptor FcγRIIb that opposes PI3K signalingin B cells develop lupus with high penetrance. FcγRIIb knockout mice(R2KO, Jackson Labs) are considered a valid model of the human diseaseas some lupus patients show decreased expression or function of FcγRIIb(S. Bolland and J. V. Ravtech 2000. Immunity 12:277-285).

The R2KO mice develop lupus-like disease with anti-nuclear antibodies,glomerulonephritis and proteinurea within about 4-6 months of age. Forthese experiments, the rapamycin analogue RAD001 (available from LCLaboratories) is used as a benchmark compound, and administered orally.This compound has been shown to ameliorate lupus symptoms in theB6.Sle1z.Sle3z model (T. Wu et al. J. Clin Invest. 117:2186-2196).

Lupus disease model mice such as R2KO, BXSB or MLR/lpr are treated atabout 2 months old, approximately for about two months. Mice are givendoses of: vehicle, RAD001 at about 10 mg/kg, or compounds disclosedherein at approximately 1 mg/kg to about 500 mg/kg. Blood and urinesamples are obtained at approximately throughout the testing period, andtested for antinuclear antibodies (in dilutions of serum) or proteinconcentration (in urine). Serum is also tested for anti-ssDNA andanti-dsDNA antibodies by ELISA. Animals are euthanized at day 60 andtissues harvested for measuring spleen weight and kidney disease.Glomerulonephritis is assessed in kidney sections stained with H&E.Other animals are studied for about two months after cessation oftreatment, using the same endpoints.

This established art model can be employed to demonstrate that thekinase inhibitors disclosed herein can suppress or delay the onset oflupus symptoms in lupus disease model mice.

Example 74 Murine Bone Marrow Transplant Assay

Female recipient mice are lethally irradiated from a γ ray source. About1 hr after the radiation dose, mice are injected with about 1×106leukemic cells from early passage p190 transduced cultures (e.g., asdescribed in Cancer Genet Cytogenet. 2005 August; 161(1):51-6). Thesecells are administered together with a radioprotective dose ofapproximately 5×10⁶ normal bone marrow cells from 3-5 wk old donor mice.Recipients are given antibiotics in the water and monitored daily. Micewho become sick after about 14 days are euthanized and lymphoid organsharvested for flow cytometry and/or magnetic enrichment. Treatmentbegins on approximately day 10 and continues daily until mice becomesick, or after a maximum of about 35 days post-transplant. Drugs aregiven by oral gavage (p.o.). In a pilot experiment a dose ofchemotherapeutic that is not curative but delays leukemia onset by aboutone week or less is identified; controls are vehicle-treated or treatedwith chemotherapeutic agent, previously shown to delay but not cureleukemogenesis in this model (e.g., imatinib at about 70 mg/kg twicedaily). For the first phase p190 cells that express eGFP are used, andpostmortem analysis is limited to enumeration of the percentage ofleukemic cells in bone marrow, spleen and lymph node (LN) by flowcytometry. In the second phase, p190 cells that express a tailless formof human CD4 are used and the postmortem analysis includes magneticsorting of hCD4+ cells from spleen followed by immunoblot analysis ofkey signaling endpoints: p Akt-T308 and S473; pS6 and p4EBP-1. Ascontrols for immunoblot detection, sorted cells are incubated in thepresence or absence of kinase inhibitors of the present disclosureinhibitors before lysis. Optionally, “phosflow” is used to detect pAkt-S473 and pS6-S235/236 in hCD4-gated cells without prior sorting.These signaling studies are particularly useful if, for example,drug-treated mice have not developed clinical leukemia at the 35 daytime point. Kaplan-Meier plots of survival are generated and statisticalanalysis done according to methods known in the art. Results from p190cells are analyzed separated as well as cumulatively.

Samples of peripheral blood (100-200 μl) are obtained weekly from allmice, starting on day 10 immediately prior to commencing treatment.Plasma is used for measuring drug concentrations, and cells are analyzedfor leukemia markers (eGFP or hCD4) and signaling biomarkers asdescribed herein.

This general assay known in the art can be used to demonstrate thateffective therapeutic doses of the compounds disclosed herein can beused for inhibiting the proliferation of leukemic cells.

Example 75 Cell Culture of Epithelial Cells of Ocular Origin

Ocular epithelial cells are obtained within 5 days postmortempost-mortem from corneas preserved under cold storage conditions inOptisol (Bausch and Lomb, Irvine, Calif.) or from corneal biopsy fromliving donors. The tissue is washed with phosphate-buffered saline andincubated in Dispase II (Roche Diagnostics, Basel, Switzerland) at 37°C. for 30 minutes, and the epithelial surface is gently scraped toseparate the epithelium from the underlying stroma. The separatedepithelium is then incubated and pipetted intrypsin-ethylenediaminetetraacetic acid to obtain a single cellsuspension. The trypsin is then neutralized with corneal epitheliumculture medium. Corneal epithelium culture medium is composed ofDulbecco modified Eagle medium:F12 basal media in a 2:1 ratio containing10% irradiated fetal bovine serum, hydrocortisone 0.4 μg/mL, choleratoxin 0.1 nmol, recombinant human insulin 5 μg/mL, and epidermal growthfactor 10 ng/mL, and the antimicrobials penicillin (100 IU/mL),streptomycin (100 μg/mL), and amphotericin B (0.25 μg/mL). Cells aremaintained by sub-culturing at a 1:4 ratio after reaching 80%confluency. Ocular epithelial cells are screened for inhibition ofproliferation or toxicity by contacting a test compound with the cellsand assaying for viability using the commercially available MTT assay(Promega).

Example 76 Cell Culture of Endothelial Cells of Ocular Origin

All tissues are maintained at 4° C. in storage medium (Optisol; ChironVision, Irvine, Calif.) for less than 10 days before study. The tissueis rinsed three times with DMEM containing 50 mg/mL gentamicin and 1.25mg/mL amphotericin B. The central cornea is removed by a trephine of8-mm diameter. Afterward, the Descemet's membrane and cornealendothelial cells are stripped from the posterior surface of theperipheral corneoscleral tissue under a dissecting microscope anddigested at 37° C. for 1.5 to 16 hours with 2 mg/mL collagenase A insupplemented hormonal epithelial medium (SHEM), which is made of anequal volume of HEPES-buffered DMEM and Ham's F12 supplemented with 5%FBS, 0.5% dimethyl sulfoxide, 2 ng/mL mouse EGF, 5 μg/mL insulin, 5μg/mL transferrin, 5 ng/mL selenium, 0.5 μg/mL hydrocortisone, 1 nMcholera toxin, 50 μg/mL gentamicin, and 1.25 μg/mL amphotericin B. Afterdigestion, HCECs formed aggregates, which are collected bycentrifugation at 2000 rpm for 3 minutes to remove the digestionsolution. As a control, Descemet's membrane strips are also digested in10 mg/mL Dispase II in SHEM and trypsin/EDTA for up to 3 hours.

Preservation of Isolated HCEC Aggregates: The resultant aggregates ofHCECs are preserved in KSFM with complete supplement (storage medium 1),DMEM/F12 with KSFM supplements (storage medium 2), or DMEM/F12 with SHEMsupplements without FBS (storage medium 3). All these media are serumfree, one of the major differences among them is the calciumconcentration, which is 0.09 mM in storage medium 1, but is 1.05 mM instorage media 2 and 3. HCEC aggregates are stored in a tissue cultureincubator at 37° C. for up to 3 weeks. Cell viability is determined(Live and Dead assay; Invitrogen) and also evaluated by subculturingthem in SHEM.

Preservation of Isolated HCEC Aggregates: The resultant HCEC aggregates,either immediately after digestion or after a period of preservation ina storage medium, are then cultured in SHEM with or without additionalgrowth factors such as 40 ng/mL bFGF, 0.1 mg/mL BPE, and 20 ng/mL NGF ona plastic dish under 37° C. and 5% CO₂. The media are changed every 2 to3 days. Some HCEC aggregates are pretreated with trypsin/EDTA at 37° C.for 10 minutes to dissociate endothelial cells before the aforementionedcultivation.

Immunostaining: HCEC aggregates are embedded in OCT and subjected tofrozen sectioning. Cryosections of 4 μm are air-dried at roomtemperature (RT) for 30 minutes, and fixed in cold acetone for 10minutes at −20° C. Sections used for immunostaining are rehydrated inPBS, and incubated in 0.2% Triton X-100 for 10 minutes. After threerinses with PBS for 5 minutes each and preincubation with 2% BSA toblock nonspecific staining, the sections are incubated with anti-laminin5, type IV collagen, perlecan, ZO-1, and connexin 43 (all at 1:100)antibodies for 1 hour. After three washes with PBS for 15 minutes, thesections are incubated with a FITC-conjugated secondary antibody (goatanti-rabbit or anti-mouse IgG at 1:100) for 45 minutes. After threeadditional PBS washes, each for 10 minutes, they are counterstained withpropidium iodide (1:1000) or Hoechst 33342 (10 μg/mL), then mounted withan antifade solution and analyzed with a fluorescence microscope. HCECscultured in 24-well plates or chamber slides are fixed in 4%paraformaldehyde for 15 minutes at RT and stained with anti-ZO-1 andconnexin 43 antibodies as just described. For immunohistochemicalstaining of Ki67, endogenous peroxidase activity is blocked by 0.6%hydrogen peroxide for 10 minutes. Nonspecific staining is blocked by 1%normal goat serum for 30 minutes. Cells are then incubated withanti-Ki67 antibody (1:100) for 1 hour. After three washes with PBS for15 minutes, cells are incubated with biotinylated rabbit anti-mouse IgG(1:100) for 30 minutes, followed by incubation with ABC reagent for 30minutes. The reaction product is developed with DAB for 5 minutes andexamined by light microscope.

Cell-Viability and TUNEL Assays: Cell-viability and terminaldeoxyribonucleotidyl transferase-mediated FITC-linked dUTP nick-end DNAlabeling (TUNEL) assays are used to determine living and apoptoticcells, respectively. HCEC aggregates are incubated with cell-viabilityassay reagents for 15 minutes at RT. Live cells are distinguished bygreen fluorescence staining of the cell cytoplasm, and dead cells arestained with red fluorescence in the nuclei. The TUNEL assay isperformed according to the manufacturer's instructions. Briefly,cross-sections of HCEC aggregates are fixed in 4% paraformaldehyde for20 minutes at RT and permeabilized with 1% Triton X-100. Samples arethen incubated for 60 minutes at 37° C. with exogenous TdT andfluorescein-conjugated dUTP, for repair of nicked 3′-hydroxyl DNA ends.Cells are treated with DNase I as the positive control, whereas negativecontrol cells are incubated with a buffer lacking the rTdT enzyme. Theapoptotic nuclei are labeled with green fluorescence.

Example 77 Cell Culture of Retinal Cells

Eyes are cut in half along their equator and the neural retina isdissected from the anterior part of the eye in buffered saline solution,according to standard methods known in the art. Briefly, the retina,ciliary body, and vitreous are dissected away from the anterior half ofthe eye in one piece, and the retina is gently detached from the clearvitreous. Each retina is dissociated with papain (WorthingtonBiochemical Corporation, Lakewood, N.J.), followed by inactivation withfetal bovine serum (FBS) and addition of 134 Kunitz units/ml of DNaseI.The enzymatically dissociated cells are triturated and collected bycentrifugation, resuspended in Dulbecco's modified Eagle's medium(DMEM)/F12 medium (Gibco BRL, Invitrogen Life Technologies, Carlsbad,Calif.) containing 25 μg/ml of insulin, 100 μg/ml of transferrin, 60 μMputrescine, 30 nM selenium, 20 nM progesterone, 100 U/ml of penicillin,100 μg/ml of streptomycin, 0.05 M Hepes, and 10% FBS. Dissociatedprimary retina 1 cells are plated onto Poly-D-lysine- and Matrigel- (BD,Franklin Lakes, N.J.) coated glass coverslips that are placed in 24-welltissue culture plates (Falcon Tissue Culture Plates, Fisher Scientific,Pittsburgh, Pa.). Cells are maintained in culture for 5 days to onemonth in 0.5 ml of media (as above, except with only 1% FBS) at 37° C.and 5% CO₂.

Immunocytochemistry Analysis: The retinal neuronal cells are culturedfor 1, 3, 6, and 8 weeks in the presence and absence of test compoundsas disclosed herein, and the cells are analyzed by immunohistochemistryat each time point. Immunocytochemistry analysis is performed accordingto standard techniques known in the art. Rod photoreceptors areidentified by labeling with a rhodopsin-specific antibody (mousemonoclonal, diluted 1:500; Chemicon, Temecula, Calif.). An antibody tomid-weight neurofilament (NFM rabbit polyclonal, diluted 1:10,000,Chemicon) is used to identify ganglion cells; an antibody to β3-tubulin(G7121 mouse monoclonal, diluted 1:1000, Promega, Madison, Wis.) is usedto generally identify interneurons and ganglion cells, and antibodies tocalbindin (AB1778 rabbit polyclonal, diluted 1:250, Chemicon) andcalretinin (AB5054 rabbit polyclonal, diluted 1:5000, Chemicon) are usedto identify subpopulations of calbindin- and calretinin-expressinginterneurons in the inner nuclear layer. Briefly, the retina 1 cellcultures are fixed with 4% paraformaldehyde (Polysciences, Inc,Warrington, Pa.) and/or ethanol, rinsed in Dulbecco's phosphate bufferedsaline (DPBS), and incubated with primary antibody for 1 hour at 37° C.The cells are then rinsed with DPBS, incubated with a secondary antibody(Alexa 488- or Alexa 568-conjugated secondary antibodies (MolecularProbes, Eugene, Oreg.)), and rinsed with DPBS. Nuclei are stained with4′,6-diamidino-2-phenylindole (DAPI, Molecular Probes), and the culturesare rinsed with DPBS before removing the glass coverslips and mountingthem with Fluoromount-G (Southern Biotech, Birmingham, Ala.) on glassslides for viewing and analysis.

Example 78 Matrigel Plug Angiogenesis Assay

Matrigel containing test compounds are injected subcutaneously orintraocularly, where it solidifies to form a plug. The plug is recoveredafter 7-21 days in the animal and examined histologically to determinethe extent to which blood vessels have entered it. Angiogenesis ismeasured by quantification of the vessels in histologic sections.Alternatively, fluorescence measurement of plasma volume is performedusing fluorescein isothiocyanate (FITC)-labeled dextran 150. The resultsare expected to indicate one or more compounds disclosed herein thatinhibit angiogenesis and are thus expected to be useful in treatingocular disorders related to aberrant angiogenesis and/or vascularpermeability.

Example 79 Corneal Angiogenesis Assay

A pocket is made in the cornea, and a plug containing an angiogenesisinducing formulation (e.g., VEGF, FGF, or tumor cells), when introducedinto this pocket, elicits the ingrowth of new vessels from theperipheral limbal vasculature. Slow-release materials such as ELVAX(ethylene vinyl copolymer) or Hydron are used to introduce angiogenesisinducing substances into the corneal pocket. Alternatively, a spongematerial is used.

The effect of putative inhibitors on the locally induced (e.g., spongeimplant) angiogenic reaction in the cornea (e.g., by FGF, VEGF, or tumorcells). The test compound is administered orally, systemically, ordirectly to the eye. Systemic administration is by bolus injection or,more effectively, by use of a sustained-release method such asimplantation of osmotic pumps loaded with the test inhibitor.Administration to the eye is by any of the methods described hereinincluding but not limited to eye drops, topical administration of acream, emulsion, or gel, intravitreal injection.

The vascular response is monitored by direct observation throughout thecourse of the experiment using a stereomicroscope in mice. Definitivevisualization of the corneal vasculature is achieved by administrationof fluorochrome-labeled high-molecular weight dextran. Quantification isperformed by measuring the area of vessel penetration, the progress ofvessels toward the angiogenic stimulus over time, or in the case offluorescence, histogram analysis or pixel counts above a specific(background) threshold.

The results can indicate one or more compounds disclosed herein inhibitangiogenesis and thus can be useful in treating ocular disorders relatedto aberrant angiogenesis and/or vascular permeability.

Example 80 Microtiter-Plate Angiogenesis Assay

The assay plate is prepared by placing a collagen plug in the bottom ofeach well with 5-10 cell spheroids per collagen plug each spheroidcontaining 400-500 cells. Each collagen plug is covered with 1100 μl ofstorage medium per well and stored for future use (1-3 days at 37° C.,5% CO₂). The plate is sealed with sealing. Test compounds are dissolvedin 200 μl assay medium with at least one well including a VEGF positivecontrol and at least one well without VEGF or test compound as anegative control. The assay plate is removed from the incubator andstorage medium is carefully pipeted away. Assay medium containing thetest compounds are pipeted onto the collagen plug. The plug is placed ina humidified incubator for (37° C., 5% CO₂) 24-48 hours. Angiogenesis isquantified by counting the number of sprouts, measuring average sproutlength, or determining cumulative sprout length. The assay can bepreserved for later analysis by removing the assay medium, adding 1 mlof 10% paraformaldehyde in Hanks BSS per well, and storing at 4° C. Theresults are expected to identify compounds that inhibit angiogenesis invarious cell types tested, including cells of ocular origin.

Example 81 Combination Use of PI3Kδ Inhibitors and Agents that InhibitIgE Production or Activity

The compounds as disclosed herein can present synergistic or additiveefficacy when administered in combination with agents that inhibit IgEproduction or activity. Agents that inhibit IgE production include, forexample, one or more of TEI-9874,2-(4-(6-cyclohexyloxy-2-napthyloxy)phenylacetamide)benzoic acid,rapamycin, rapamycin analogs (i.e., rapalogs), TORC1 inhibitors, TORC2inhibitors, and any other compounds that inhibit mTORC1 and mTORC2.Agents that inhibit IgE activity include, for example, anti-IgEantibodies such as Omalizumab and TNX-901.

One or more of the subject compounds capable of inhibiting PI3Kδ can beefficacious in treatment of autoimmune and inflammatory disorders(AIID), for example, rheumatoid arthritis. If any of the compoundscauses an undesired level of IgE production, one can choose toadminister it in combination with an agent that inhibits IgE productionor IgE activity. Additionally, the administration of PI3Kδ or PI3Kδ/γinhibitors as disclosed herein in combination with inhibitors of mTORcan also exhibit synergy through enhanced inhibition of the PI3Kpathway. Various in vivo and in vitro models can be used to establishthe effect of such combination treatment on AIID including but notlimited to (a) in vitro B-cell antibody production assay, (b) in vivoTNP assay, and (c) rodent collagen induced arthritis model.

(a) B-Cell Assay

Mice are euthanized, and the spleens are removed and dispersed through anylon mesh to generate a single-cell suspension. The splenocytes arewashed (following removal of erythrocytes by osmotic shock) andincubated with anti-CD43 and anti-Mac-1 antibody-conjugated microbeads(Miltenyi Biotec). The bead-bound cells are separated from unbound cellsusing a magnetic cell sorter. The magnetized column retains the unwantedcells and the resting B cells are collected in the flow-through.Purified B-cells are stimulated with lipopolysaccharide or an anti-CD40antibody and interleukin 4. Stimulated B-cells are treated with vehiclealone or with PI3Kδ inhibitors as disclosed herein with and without mTORinhibitors such as rapamycin, rapalogs, or mTORC1/C2 inhibitors. Theresults are expected to show that in the presence of mTOR inhibitors(e.g., rapamycin) alone, there is little to no substantial effect on IgGand IgE response. However, in the presence of PI3Kδ and mTOR inhibitors,the B-cells are expected to exhibit a decreased IgG response as comparedto the B-cells treated with vehicle alone, and the B-cells are expectedto exhibit a decreased IgE response as compared to the response fromB-cells treated with PI3Kδ inhibitors alone.

(b) TNP Assay

Mice are immunized with TNP-Ficoll or TNP-KHL and treated with: vehicle,a PI3Kδ inhibitor, an mTOR inhibitor, for example rapamycin, or a PI3Kδinhibitor in combination with an mTOR inhibitor such as rapamycin.Antigen-specific serum IgE is measured by ELISA using TNP-BSA coatedplates and isotype specific labeled antibodies. It is expected that micetreated with an mTOR inhibitor alone exhibit little or no substantialeffect on antigen specific IgG3 response and no statisticallysignificant elevation in IgE response as compared to the vehiclecontrol. It is also expected that mice treated with both PI3Kδ inhibitorand mTOR inhibitor exhibit a reduction in antigen specific IgG3 responseas compared to the mice treated with vehicle alone. Additionally, themice treated with both PI3Kδ inhibitor and mTOR inhibitor exhibit adecrease in IgE response as compared to the mice treated with PI3Kδinhibitor alone.

(c) Rat Collagen Induced Arthritis Model

Female Lewis rats are anesthetized and given collagen injectionsprepared and administered as described previously on day 0. On day 6,animals are anesthetized and given a second collagen injection. Calipermeasurements of normal (pre-disease) right and left ankle joints areperformed on day 9. On days 10-11, arthritis typically occurs and ratsare randomized into treatment groups. Randomization is performed afterankle joint swelling is obviously established and there is good evidenceof bilateral disease.

After an animal is selected for enrollment in the study, treatment isinitiated. Animals are given vehicle, PI3Kδ inhibitor, or PI3Kδinhibitor in combination with rapamycin. Dosing is administered on days1-6. Rats are weighed on days 1-7 following establishment of arthritisand caliper measurements of ankles taken every day. Final body weightsare taken on day 7 and animals are euthanized.

The combination treatment using a compound as disclosed herein andrapamycin can provide greater efficacy than treatment with PI3Kδinhibitor alone.

Example 82 Delayed Type Hypersensitivity Model

DTH was induced by sensitizing 60 BALB/c male mice on day 0 and day 1with a solution of 0.05% 2,4 dinitrofluorobenzene (DNFB) in a 4:1acetone/olive oil mixture. Mice were gently restrained while 20 μL ofsolution was applied to the hind foot pads of each mouse. The hind footpads of the mice were used as they represent an anatomical site that canbe easily isolated and immobilized without anesthesia. On day 5, micewere administered a single dose of vehicle, IPI-145 at 10, 3, 1, or 0.3mg/kg, or dexamethasone at a dose of 5 mg/kg by oral gavage. Thirtyminutes later mice were anaesthetized, and a solution of 0.25% DNFB in a4:1 acetone/olive oil solution was applied to the left inner and outerear surface. This application resulted in the induction of swelling tothe left ear and under these conditions, all animals responded to thistreatment with ear swelling. A vehicle control solution of 4:1acetone/olive oil was applied to the right inner and outer ear. Twentyfour hours later, mice were anaesthetized, and measurements of the leftand right ear were taken using a digital micrometer. The differencebetween the two ears was recorded as the amount of swelling induced bythe challenge of DNFB. Drug treatment groups were compared to vehiclecontrol to generate the percent reduction in ear swelling. Dexamethasoneis routinely used as a positive control as it has broadanti-inflammatory activity.

Example 83 Peptidoglycan-Polysaccharide Rat Arthritic Model

(a) Systemic Arthritis Model

All injections are performed under anesthesia. 60 female Lewis rats(150-170) are anesthetized by inhalation isoflurane using a small animalanesthesia machine. The animals are placed in the induction chamberuntil anesthetized by delivery of 4-5% isoflurane in O₂ and then held inthat state using a nose cone on the procedure table. Maintenance levelof isoflurane is at 1-2%. Animals are injected intraperitoneally (i.p.)with a single injection of purified PG-PS 10S Group A, D58 strain(concentration 25 ug/g of bodyweight) suspended in sterile 0.85% saline.Each animal receives a total volume of 500 microliters administered inthe lower left quadrant of the abdomen using a 1 milliliter syringe witha 23 gauge needle. Placement of the needle is critical to avoidinjecting the PG-PS 10S into either the stomach or caecum. Animals areunder continuous observation until fully recovered from anesthesia andmoving about the cage. An acute response of a sharp increase in anklemeasurement, typically 20% above baseline measurement can peak in 3-5days post injection. Treatment with test compounds can be PO, SC, IV orIP. Rats are dosed no more than two times in a 24 hour time span.Treatment can begin on day 0 or any day after that through day 30. Theanimals are weighed on days 0, 1, 2, 3, 4, 5, 6, 7 and beginning againon day 12-30 or until the study is terminated. Paw/ankle diameter ismeasured with a digital caliper on the left and right side on day 0prior to injection and again on day 1, 2, 3, 4, 5, 6 and 7. On day 12,measurements begin again and continue on through day 30. At this time,animals can be anesthetized with isoflurane, as described above, andterminal blood samples can be obtained by tail vein draws for theevaluation of the compound blood levels, clinical chemistry orhematology parameters. Animals are them euthanized with carbon dioxideoverdose. A thoracotomy can be conducted as a means of deathverification.

(b) Monoarticular Arthritis Model

All injections are performed under anesthesia. 60 female Lewis rats(150-170) are anesthetized by inhalation isoflurane using a small animalanesthesia machine. The animals are placed in the induction chamberuntil anesthetized by delivery of 4-5% isoflurane in O₂ and then held inthat state using a nose cone on the procedure table. Maintenance levelof isoflurane is at 1-2%. Animals are injected intra-articular (i.a.)with a single injection of purified PG-PS 100P Group A, D58 strain(concentration 500 ug/mL) suspended in sterile 0.85% saline. Each ratreceives a total volume of 10 microliters administered into thetibiotalar joint space using a 1 milliliter syringe with a 27 gaugeneedle. Animals are under continuous observation until fully recoveredfrom anesthesia and moving about the cage. Animals that respond 2-3 dayslater with a sharp increase in ankle measurement, typically 20% abovebaseline measurement on the initial i.a. injection, are included in thestudy. On day 14, all responders are anesthetized again using theprocedure previously described. Animals receive an intravenous (I.V.)injection of PG-PS (concentration 250 uL/mL). Each rat receives a totalvolume of 400 microliters administered slowly into the lateral tail veinusing a 1 milliliter syringe with a 27 gauge needle. Baseline anklemeasurements are measured prior to IV injection and continue through thecourse of inflammation or out to day 10. Treatment with test compoundswill be PO, SC, IV or IP. Rats are dosed no more than two times in a 24hour time span. Treatment can begin on day 0 or any day after thatthrough day 24. The animals are weighed on days 0, 1, 2, 3, 4, 5, andbeginning again on day 14-24 or until the study is terminated. Paw/anklediameter is measured with a digital caliper on the left and right sideon day 0 prior to injection and again on day 1, 2, 3, 4, 5, andbeginning again on day 14-24 or until the study is terminated. At thistime, animals can be anesthetized with isoflurane, as described above,and terminal blood samples can be obtained by tail vein draws for theevaluation of the compound blood levels, clinical chemistry orhematology parameters. Animals are them euthanized with carbon dioxideoverdose. A thoracotomy can be conducted as a means of deathverification.

What is claimed is:
 1. A compound of formula (Ib):

or pharmaceutically acceptable forms thereof, wherein B is hydrogen,alkyl, amino, heteroalkyl, or a moiety of Formula II:

wherein W_(c) is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl; q isan integer of 0, 1, 2, 3, or 4; X is absent or —(CH(R⁹))_(z)—, and z isan integer of 1, 2, 3, or 4; Y is absent, —O—, —S—, —S(═O)—, —S(═O)₂,—C(═O)—, —C(═O)(CHR⁹)_(z)—, —N(R⁹)—, N(R⁹)—C(═O)—, —N(R⁹)—C(═O)NH—, or—N(R⁹)C(R⁹)₂—, and z is an integer of 1, 2, 3, or 4; R¹ is hydrogen,alkyl, alkenyl, alkynyl, alkoxy, amido, alkoxycarbonyl, sulfonamido,halo, cyano, or nitro; each R² is independently alkyl, alkenyl, alkynyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, arylalkyl,heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl,sulfonamido, halo, cyano, hydroxy, nitro, phosphate, urea, or carbonate;R³ is cycloalkyl, cycloalkylalkyl, aryl, heteroaryl, heterocyclyl,aralkyl, heteroaralkyl, heterocyclylalkyl, alkenyl, or alkynyl, or R³ isa heteroatom selected from N, S, and O, wherein the heteroatom has acovalent bond either directly or through a C₁-C₆ alkyl group to an aryl,heteroaryl or heterocyclyl, or R³ and R⁵ are taken together with thecarbons to which they are attached form a 5- or 6-membered ring; whereineach of the above substituents can be substituted with 0, 1, 2, or 3R¹³; R⁵, R⁶, R⁷, and R⁸ are independently hydrogen, halo, cyano, alkylor amino; each R⁹ is independently hydrogen, alkyl, or heterocycloalkyl;W_(d) is

R¹¹ is hydrogen, alkyl, halo, amino, amido, hydroxy, alkoxy, phosphate,urea, or carbonate; R¹² is hydrogen, alkyl, haloalkyl, alkynyl, alkenyl,halo, —C(O)NH₂, aryl, heteroaryl, nonaromatic heterocyclyl, orcycloalkyl, R^(a′) is hydrogen, alkyl, —NH₂, cyano or halogen; and eachR¹³ is independently hydrogen, C₁-C₆ alkyl, C₁-C₆ alkoxy or halogen. 2.The compound of claim 1, wherein R³ is a 5-membered heteroaryl; a5-membered nonaromatic heterocycle; a 6-membered aryl; a 6-memberedheteroaryl or a 6-membered nonaromatic heterocycle.
 3. The compound ofclaim 1, wherein R³ is


4. The compound of claim 1, wherein B is a moiety of Formula II:


5. The compound of claim 4, wherein W_(c) is 6-membered aryl orcycloalkyl.
 6. The compound of claim 5, wherein q is 0 or
 1. 7. Thecompound of claim 6, wherein R¹ is hydrogen, alkyl, alkoxy, amido, halo,cyano, or nitro.
 8. The compound of claim 6, wherein q is 1 and R² isalkyl, cycloalkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy,amino, halo, cyano, hydroxy or nitro.
 9. The compound of claim 1,wherein Y is —O—, —S(═O)₂, —C(═O)—, —N(R⁹)— or N(R⁹)—C(═O)—.
 10. Thecompound of claim 1, wherein X is —(CH(R⁹))_(z)—.
 11. The compound ofclaim 10, wherein z is 1, 2 or
 3. 12. The compound of claim 10, whereinR⁹ is hydrogen or alkyl.
 13. The compound of claim 1, wherein W_(d) is


14. The compound of claim 1, wherein R⁶ is hydrogen, halo, cyano oralkyl.
 15. The compound of claim 1, wherein R⁷ is hydrogen, halo, cyanoor alkyl.
 16. The compound of claim 1, wherein R⁸ is hydrogen, halo,cyano or alkyl.
 17. A pharmaceutical composition comprising a compoundaccording to claim 1 and one or more pharmaceutically acceptableexcipients.
 18. A method of treating a PI3K mediated disorder in asubject, the method comprising administering a therapeutically effectiveamount a compound according to claim 1 or a pharmaceutical compositionaccording to claim 17 to said subject.
 19. The method of claim 18,wherein the disorder is cancer, an inflammatory disease or anauto-immune disease.
 20. A method of treating a PI3K mediated disorderin a subject, the method comprising administering a therapeuticallyeffective amount of a compound according to claim 1 or a pharmaceuticalcomposition according to claim 17 to said subject.
 21. The method ofclaim 20, wherein the disorder is cancer, an inflammatory disease or anauto-immune disease.